
1. Sequencing of patient tumor samples and cancer cell lines for endotype identification in multiple cancer types
(Submitter supplied) DNA and RNA were isolated from snap frozen or FFPE primary tumor tissue, or from cultured and preserved cell cultures. All sequencing was performed at the Beijing Genomics Institute.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL23227 GPL15433 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE138nnn/GSE138269/
Series		Accession: GSE138269	ID: 200138269

2. mRNA sequencing of highly and lowly metastatic human colorectal cancer PDXs
(Submitter supplied) We performed in-vivo selection of human patient derived colorectal cancer xenografts. 4 independent highly-liver metastatic sub-lines (lvm PDXs) were generated. Those lvm PDXs were harvested with the corresponding parental PDX tumors from mice and then we performed MACS mice cell depletion followed by FACS sorting to obtain human EpCAM positive and mice MHC negatitve populations. total RNA was extracted from those ex-vivo tumors and high-throuput sequencing was performed
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (FPKM_TRACKING, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE138nnn/GSE138248/
Series		Accession: GSE138248	ID: 200138248

3. Electrical and synaptic integration of glioma into neural circuits
(Submitter supplied) We report single cell RNA-seq data from patient-derived xenografts that were dissociated, FACS sorted into 96-well plates and profiled by Smart-seq2 and sequencing on an Illumina NextSeq500
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 384 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134269/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA554601
Series		Accession: GSE134269	ID: 200134269

4. Identification of the role of polydom in neurofibromas
(Submitter supplied) Dermal neurofibromas in von Recklinghausen's disease (vRD) develop in the dermis. Therefore, we hypothesized that a dermal niche exists that promotes the development of dermal neurofibromas in subjects with vRD. We focused on polydom, a ligand for integrin α9β1 and known as a factor expressed in the nerve tissue of mice and human breast cancer and lung cancer, which is expressed around nerve tissue. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117322/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481758
Series		Accession: GSE117322	ID: 200117322

5. GIRK1 triggers multiple cancer-related pathways in the benign mammary epithelial cell line MCF10A
(Submitter supplied) Excessive expression of subunit 1 of GIRK1 in ER+ breast tumors is associated with reduced survival times, and increased lymph node metastasis in patients. To investigate possible tumor-initiating properties, benign MCF10A and malign MCF7 mammary epithelial cells overexpressing GIRK1 were engineered, neoplasia associated vital parameters and resting potentials were measured and compared to controls. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23934 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE138nnn/GSE138155/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA574941
Series		Accession: GSE138155	ID: 200138155

6. High level DNA repair gene expression in human ES cells
(Submitter supplied) Many studies have reported that human embryonic stem (hES) cells have an exceptional ability to repair damaged DNA. Moreover, unlike differentiated cells, hES cells have features and mechanisms such as apoptosis prone mitochondria, which prevent any changes in genetic information caused by DNA damage to be transmitted to their descendants. Type-A (dark) spermatogonia and cancer stem cells are thought to be dormant. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 7 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE138nnn/GSE138093/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA574579
Series		Accession: GSE138093	ID: 200138093

7. CAR T cells Overexpressing cJun Are Exhaustion-Resistant and   Mediate Enhanced Antitumor Activity
(Submitter supplied) CAR T cells mediate antitumor effects in a small subset of cancer patients, but dysfunction due to T cell exhaustion is an important barrier to progress.  To investigate the biology of exhaustion in human T cells expressing CAR receptors, we used a model system employing a tonically signaling CAR, which induces hallmarks of exhaustion described in other settings.  Exhaustion was associated with a profound defect in IL-2 production alongside increased chromatin accessibility of AP-1 transcription factor motifs, and overexpression of numerous bZIP and IRF transcription factors that have been implicated in inhibitory activity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 24 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136891/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA563926
Series		Accession: GSE136891	ID: 200136891

8. Single-cell gene expression in Her2-specific CAR T cells in osteosarcoma mouse model.
(Submitter supplied) Purpose: To compare cell states between control Her2-BBz and JUN-overexpression Her2-BBz human CAR T cells in a mouse model of osteosarcoma. Methods: 8-week old NSG mice were implanted with 1 million 143B osteosarcoma tumor cells intramuscularly in the right leg. 14 days post tumor implantation, mice were infused intravenously with 10 million human CAR+ T cells via tail vein injection. Before T cell transfer, mice were randomized for tumor size and treated with either control Her2-BBz or JUN-overexpressing Her2-BBz CAR T cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (H5, HTML, RDS, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136805/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA563699
Series		Accession: GSE136805	ID: 200136805

9. ADP-ribosylation Levels Correlate with Gene Expression Patterns and Clinical Outcomes in Ovarian Cancers
(Submitter supplied) Inhibitors of nuclear poly(ADP-ribose) polymerase (PARP) enzymes (e.g., PARP-1) have improved clinical outcomes in ovarian cancer, especially in patients with BRCA1/2 gene mutations or additional homologous recombination (HR) DNA repair pathway deficiencies.  These defects serve as biomarkers for response to PARP inhibitors (PARPi).  We sought to identify an additional biomarker that could predict responses to both conventional chemotherapy and PARPi in ovarian cancers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 22 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136155/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA561401
Series		Accession: GSE136155	ID: 200136155

10. ETS family proteins bind glucocorticoid receptor: relevance for treatment of Ewing sarcoma
(Submitter supplied) Differential expression of gene was analyzed after FLI1 silencing in Ewing Sarcoma cell line A673.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135229/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA558012
Series		Accession: GSE135229	ID: 200135229

11. Identification of miR-194-5p target genes in gastric cancer
(Submitter supplied) Increasing studies report that miR-194-5p plays a tumor suppressor role in gastric cancer (GC). Previous studies have revealed that miR-194 inhibited gastric cancer progression through different pathways by affecting the expression level of different target genes. For example, miR-194 have been reported to be able to regulate the expression of FOXM1, NR2F2, BMI1, SDAD1, RBX1, KDM5B, ZEB1 and AKT2 etc. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134308/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA554679
Series		Accession: GSE134308	ID: 200134308

12. High-depth RNA sequencing of isogenic wild-type, PIK3CA-WT/H1047R and PIK3CA-H1047R/H1047R human iPSCs
(Submitter supplied) We used CRISPR/Cas9 to knock in the cancer "hotspot" mutation PIK3CA-H1047R into one or both alleles of a wild-type induced pluripotent stem cell (iPSC) line (WTC11; Coriell # GM25256; P37-P38). Four cultures from each genotype (3 wild-type clones, 3 heterozygous clones, 2 homozygous clones) were subjected to paired-end mRNA sequencing (mean read length = 150 bp). The aim of this experiment was to confirm and expand upon previous transcriptomic results suggesting a near-binary transcriptional effect in homozygous versus heterozygous PIK3CA-H1047R iPSCs (publication doi: 10.1073/pnas.1821093116). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134076/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA553693
Series		Accession: GSE134076	ID: 200134076

13. Blood extracellular vesicle long RNA sequencing of human blood from pancreatic ductal adenocarcinoma (PDAC), chronic pancreatitis (CP) and healthy individuals
(Submitter supplied) Blood samples were collected from all participants in 10-mL EDTA-coated Vacutainer tubes. Plasma was separated by centrifugation at 3,000 rpm for 10 min at room temperature (25°C) within 2 h after blood collection and then centrifuged at 13,000 rpm for 10 min at 4°C to remove debris. Isolated plasma samples were stored at -80°C until use. EV RNA were isolated by affinity-based binding to spin columns using an exoRNeasy Serum/Plasma kit (Qiagen, Hilden, Germany). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL20795 501 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133684/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA552230
Series		Accession: GSE133684	ID: 200133684

14. Deconvolution of myeloid cell cytokine specific transcriptional profiles during tuberculosis and cancer identifies neutrophil activation as a prognostic feature
(Submitter supplied) The cytokine environment and cellular infiltrate during an inflammatory response may contain prognostic features that could guide therapy or predict disease outcome. Here we analyzed the transcriptional responses of human monocytes, macrophages, dendritic cells and neutrophils to stimulation by type 1 cytokines (IFN-g, IFN-b and IFN-l) type 2 cytokines (IL-4 and IL-13) and the immunoregulatory cytokine IL-10. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 84 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131990/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA545516
Series		Accession: GSE131990	ID: 200131990

15. Global transcriptional profiling changes upon knockout of USP22 in human Non-small cell lung cancer cells
(Submitter supplied) The experiment was designed to display differential gene expression profiling changes in two human non-small cell lung cancer cells A549 and H1299 upon knockout of USP22 gene, by using RNAseq technology.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131934/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA545343
Series		Accession: GSE131934	ID: 200131934

16. A novel lncRNA lncRNA-AK096729 promotes colorectal carcinogenesis and glucose metabolism by stabilizing and specifying the transcription modification pattern of c-Myc
(Submitter supplied) To elucidate whether  lncRNA-AK096729 plays a role in  colorectal cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of  lncRNA-AF339830 siRNA and control siRNA transfectants.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129950/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA533256
Series		Accession: GSE129950	ID: 200129950

17. ELF4 is a target of miR-124 and promotes neuroblastoma proliferation and undifferentiated state
(Submitter supplied) We performed RNA-seq to identify the transcriptional targets of ELF4 in BE-(2)-C neuroblastoma cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125772/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA517477
Series		Accession: GSE125772	ID: 200125772

18. Role for citron kinase in prostate cancer growth
(Submitter supplied) To study the effect of siRNA-mediated CIT silencing on androgen-responsive genes in LNCaP cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123970/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510399
Series		Accession: GSE123970	ID: 200123970

19. The mithralog EC-7072 is highly cytotoxic to chronic lymphocytic leukemia cells by targeting the B-cell receptor signaling pathway
(Submitter supplied) EC-7072, an analogue of Mithramycin A, exerts a direct cytotoxic effect on primary leukemic cells from patients with chronic lymphocytic leukemia (CLL) in vitro. To elucidate the underlying mechanisms mediating this effect, RNA sequencing was carried out employing total RNA from primary leukemic cells exposed to EC-7072. Data analysis revealed a dramatic impact of the compound on the transcriptional profile of CLL cells, unraveling a modulation of key mediators associated to homeostasis and survival of CLL cells, including B-cell receptor signaling. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 16 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123777/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509792
Series		Accession: GSE123777	ID: 200123777

20. Role of iron in the regulation of the epithelial-to-mesenchymal transition
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL24676 14 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121664/
Series		Accession: GSE121664	ID: 200121664

21. Role of iron in the regulation of the epithelial-to-mesenchymal transition (RNA-seq)
(Submitter supplied) The biological process termed Epithelial-to-Mesenchymal Transition (EMT) plays a central role in cancer cell invasion, metastasis, self-renewal and resistance to therapy1,2. Here, we characterize using RNA sequencing  the mRNA levels changes occurring during EMT induced by epidermal growth factor in breast cancer MDA-MB-468 cells.  1. Nieto, M. A., Huang, R. Y., Jackson, R. A. & Thiery, J. P. EMT: 2016. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121663/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA498058
Series		Accession: GSE121663	ID: 200121663

22. Mutant KRAS/BRAF Reprograms the Enhancer Landscape via GATA1 to Drive Chemoresistance
(Submitter supplied) Despite advances in the detection and management of colorectal cancers, resistance to anti-cancer therapies remains a significant challenge. Activating mutations in KRAS and BRAF are frequently observed in colorectal cancers and have been associated with aggressive tumors and poor survival after chemotherapy. In the present study, we demonstrate that mutations in KRAS/BRAF alter the enhancer landscape of tumor cells, which leads to the resistance of the cornerstone colorectal cancer chemotherapeutic agent 5-fluorouracil (5-FU) through activation of transcription factor GATA1. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL20301 GPL20795 26 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115400/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474834
Series		Accession: GSE115400	ID: 200115400

23. Transcriptome analysis of peripheral blood monocytes
(Submitter supplied) RNA sequencing data of peripheral blood monocytes to assess their transcriptomic differences, in particular metabolics, compared to ascites fluid-derived tumor associated macrophages (datasets publicly available; E-MTAB-3167 and E-MTAB-4162)
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89187/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA350561
Series		Accession: GSE89187	ID: 200089187

24. Identification of Notch1 regulated genes in A549 NSCLC cell line
(Submitter supplied) Notch signaling is an evolutionarily conserved signaling pathway. Notch1 signaling has been shown to potentially paly an important role in cancer development and progression. To illustrate the underlying regulating mechanisms of Notch1 activation in NSCLC, the intracellular domain of Notch1 receptor (NICD1) was overexpressed in A549 cell line and the RNA-sequences were performed.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137106/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA564556
Series		Accession: GSE137106	ID: 200137106

25. Radiomic and transcriptomic analysis for understanding metastatic clear cell renal cell carcinoma
(Submitter supplied) To understand the relationship of radiomic and transcriptomic features of metastatic clear cell renal cell carcinoma, we performed RNA-sequencing in clear cell renal cell carcinomas (ccRCCs).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 19 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135091/
Series		Accession: GSE135091	ID: 200135091

26. A novel target of EZH1/2 for treatment of mantle cell lymphoma
(Submitter supplied) Mantle cell lymphoma (MCL) is a rare subtype of non-Hodgkin’s lymphoma, which is characterized by the translocation of t(11:14)(q13;q32) resulting in overexpression of cyclin D1. Patients with MCL often acquire resistance to conventional chemotherapy such as R-CHOP, BR, and ibrutinib. Therefore, novel therapeutic targets for relapsed MCL are needed. EZH1/2 are catalytic components of PRC2, which trimethylates H3K27 to repress transcription of target genes and play critical roles in B-cell development. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123518/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA508977
Series		Accession: GSE123518	ID: 200123518

27. Transcriptomic analysis of gastric cancer cells in response to stable over-expression of circular RNA derived from CTNNB1 gene (circ-CTNNB1)
(Submitter supplied) Circular RNAs (circRNAs), a subclass of noncoding RNAs characterized by covalently closed continuous loops, play emerging roles in tumorigenesis and aggressiveness. However, the functions and underlying mechanisms of circRNAs in regulating the Wnt/β-catenin signaling and cancer progression still remain elusive. We identify one intronic circRNA derived from CTNNB1 (circ-CTNNB1) as a novel driver of cancer progression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120496/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA493202
Series		Accession: GSE120496	ID: 200120496

28. Transcriptional signature of lymphoblastoid cell lines of BRCA1, BRCA2 and non-BRCA1/2 high risk breast cancer families
(Submitter supplied) Approximately 25% of hereditary breast cancer cases associated with a strong familial history can be explained by mutations in BRCA1 or BRCA2 and other lower penetrance genes. The remaining high-risk families could be classified as BRCAX (non-BRCA1/2) families, in which no penetrant mutation has been found until now. Gene expression involving alternative splicing represents a well-known mechanism regulating the expression of multiple transcripts encoded by individual genes, which could be involved in cancer development. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 121 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87080/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA343467
Series		Accession: GSE87080	ID: 200087080

29. The ultra-sensitive Nodewalk technique identifies stochastic from virtual, population-based enhancer hubs regulating MYC in 3D: Implications for the fitness of cancer cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Drosophila melanogaster
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
4 related Platforms 98 Samples
FTP download: GEO (BED, TAB, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76049/
Series		Accession: GSE76049	ID: 200076049

30. The ultra-sensitive Nodewalk technique identifies stochastic from virtual, population-based enhancer hubs regulating MYC in 3D: Implications for the fitness of cancer cells [GRO-seq]
(Submitter supplied) The relationship between stochastic transcriptional bursts and dynamic 3D chromatin states is not well understood due to poor sensitivity and/or resolution of current chromatin structure-based assays. Consequently, it is not well established if enhancers operate individually and/or in clusters to coordinate gene transcription. In the current study, we introduce Nodewalk, which uniquely combines high sensitivity with high resolution to enable the analysis of chromatin networks in minute input material. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76043/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA306057
Series		Accession: GSE76043	ID: 200076043

31. The ultra-sensitive Nodewalk technique identifies stochastic from virtual, population-based enhancer hubs regulating MYC in 3D: Implications for the fitness of cancer cells [RNA-seq]
(Submitter supplied) The relationship between stochastic transcriptional bursts and dynamic 3D chromatin states is not well understood due to poor sensitivity and/or resolution of current chromatin structure-based assays. Consequently, it is not well established if enhancers operate individually and/or in clusters to coordinate gene transcription. In the current study, we introduce Nodewalk, which uniquely combines high sensitivity with high resolution to enable the analysis of chromatin networks in minute input material. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76041/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA306058
Series		Accession: GSE76041	ID: 200076041

32. Transcriptome analysis of Enzalutamide-resistant C4-2B (C4-2B MDVR) cells treated with Indocin.
(Submitter supplied) The overall goal of this study was to identify genes that were differentially-expressed in C4-2B MDVR cells treated with Indocin. C4-2B MDVR were either treated with Indocin (20 uM) or DMSO vehicle control for 3 days, followed by isolation of total cellular RNA. Transcriptome analysis was performed with RNA-Sequencing (RNA-Seq) in order to identify differentially-expressed genes (DEGs) induced by Indocin treatment.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129596/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA531908
Series		Accession: GSE129596	ID: 200129596

33. FOXA1 Chromatin Binding is Regulated by LSD1-Mediated Demethylation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 46 Samples
FTP download: GEO (BW, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114268/
Series		Accession: GSE114268	ID: 200114268

34. RNA-Seq with DHT induction and/or GSK treatment at 24, 48 hrs and 2 weeks
(Submitter supplied) The major pioneer factor activity of FOXA1 in PCa is to facilitate AR recruitment to androgen-regulated enhancers. Therefore, we hypothesized that the decreased FOXA1 binding and enhancer availability by LSD1 inhibition may result in the impairment of subsequent AR recruitment to enhancers. To globally test this hypothesis, we performed AR ChIP-seq in LNCaP cells treated with an LSD1 inhibitors. Consistent with previous reports, DHT treatment can dramatically induce AR binding to chromatin. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114267/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA470714
Series		Accession: GSE114267	ID: 200114267

35. An evolutionarily conserved function of polycomb silences the MHC class I antigen presentation pathway and enables immune evasion in cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus; Sarcophilus harrisii
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 GPL26397 54 Samples
FTP download: GEO (BROADPEAK, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129382/
Series		Accession: GSE129382	ID: 200129382

36. An evolutionarily conserved function of polycomb silences the MHC class I antigen presentation pathway and enables immune evasion in cancer [RNA-Seq]
(Submitter supplied) Loss of MHC class I (MHC-I) antigen presentation in cancer cells can lead to immunotherapy resistance. Using a genome-wide CRISPR/Cas9 screen we identify a critical role for polycomb repressive complex 2 (PRC2) in the coordinated transcriptional silencing of the MHC-I antigen processing pathway (MHC-I APP). This evolutionarily conserved function of PRC2 promotes evasion of T-cell mediated immunity, enabling tumour transmission to non-histocompatible recipients in small cell lung cancer (SCLC) and Tasmanian Devil Facial Tumour. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129381/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA531104
Series		Accession: GSE129381	ID: 200129381

37. Identification of YTHDF1 targeted m6A modified transcripts in lung cancer cells
(Submitter supplied) In addition to perform the m6A-seq in A549 cells, we sequenced RNA obtained from the immuno-purified complex of YTHDF1 (RIP-seq) to reveal YTHDF1 bound mRNAs, 3,676 genes were shared (m6A-seq+RIP-seq) as high-confident targets of YTHDF1 , which were mapped to cell cycle and tumor (including lung cancer) related signaling pathways in the KEGG pathway database
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL20301 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136433/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA562532
Series		Accession: GSE136433	ID: 200136433

38. Identification of drivers and therapeutic vulnerabilities in anti-androgen resistant prostate cancer cells
(Submitter supplied) Inhibition of the androgen receptor (AR) by anti-androgens is the standard treatment for castration resistant prostate cancer (CRPC), but it inevitably leads to the development of resistance. We generated two multi anti-androgen resistant cell-line models by treatment of LNCaP cells with enzalutamide (ResA) and RD-162 (ResB). Both cell-lines have an AR independent, non-neuroendocrine phenotype. To identify the resistance mechanisms we performed RNASeq analysis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 42 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130534/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540539
Series		Accession: GSE130534	ID: 200130534

39. The lung-enriched p53 mutants V157F and R158L/P regulate a novel transcriptome in lung cancer
(Submitter supplied) Lung cancer is the leading cause of cancer-related deaths in the US, and alterations in the tumor suppressor gene TP53 are the most frequent somatic mutation among all histologic subtypes of lung cancer. Mutations in TP53 frequently result in a protein that exhibits not only loss of tumor suppressor capability but also gain of oncogenic function (GOF). The canonical p53 hotspot mutants R175H and R273H, for example, confer upon tumors a metastatic phenotype in murine models of mutant p53. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120534/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA493296
Series		Accession: GSE120534	ID: 200120534

40. Re-programing chromatin with a bifunctional LSD1/HDAC inhibitor induces therapeutic differentiation in DIPG [RNA-seq]
(Submitter supplied) Histone H3 lysine 27 to methionine mutations (H3K27M) resulting in aberrant chromatin regulation are frequently observed in Diffuse Intrinsic Pontine Glioma (DIPG), a pediatric brain tumor with no cure. We conducted a CRISPR screen to determine if various chromatin regulators might be targeted to treat DIPG. Excitingly, this genetic screen reveals that co-targeting lysine specific demethylase 1 (LSD1) and histone deacetylases (HDACs) results in an enhanced growth suppressive effect in patient DIPG cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110571/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434042
Series		Accession: GSE110571	ID: 200110571

41. Next generation sequencing facilitates transcriptome analyses of mock and NCCRP1 transfected esophageal squamous cell carcinoma cell line KYSE150 cells
(Submitter supplied) We obtained transcriptome profiling (RNA-seq) of human esophageal squamous cell carcinoma cell line KYSE150 stabley transfected clones with pIRES2-EGFP vector or human NCCRP1-expression vector by using next generation sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 6 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87665/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345502
Series		Accession: GSE87665	ID: 200087665

42. Next generation sequencing facilitates transcriptome analyses of mock and RHCG transfected esophageal squamous cell carcinoma cell line KYSE30 cells
(Submitter supplied) We obtained transcriptome profiling (RNA-seq) of human esophageal squamous cell carcinoma cell line KYSE30 cells stabley transfected with pIRES2-EGFP vector or human RHCG-expression vector by using next generation sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 2 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87664/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345505
Series		Accession: GSE87664	ID: 200087664

43. Identification of a LIF-responsive replication-competent human β cell
(Submitter supplied) The beta (β) cell mass formed during embryogenesis is amplified by cell replication that occurs primarily during fetal and early postnatal development. Thereafter, β cells become functionally mature and their mass is maintained by a very low rate of replication.  For those few β cells that replicate in adult life, it is not known how replication is initiated, uncoupled from β cell function nor whether this occurs in a specialized subset of β cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 14 Samples
FTP download: GEO (H5, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137961/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA573954
Series		Accession: GSE137961	ID: 200137961

44. VEGF-A drives T cell exhaustion in anti-PD-1-resistant microsatellite stable colorectal cancers
(Submitter supplied) VEGF-A drives T-cell exhaustion via TOX-dependent transcriptional programming in microsatellite stable colorectal cancers.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135798/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA560084
Series		Accession: GSE135798	ID: 200135798

45. Genetic determinants of venetoclax resistance
(Submitter supplied) Resistance to the first approved BCL-2 inhibitor venetoclax is emerging in lymphoid malignancies. The study aimed to identify the genetic determinants of such resistance. From genome-scale screens we determined the genes influencing the sensitivity to BCL-2 inhibition. The present set of data is related to expression changes (assessed by RNA sequencing) observed in the resistant OCI-Ly1 lymphoma cell line as well as those resulting from genetic perturbation (using CRISPR-Cas9) targeting the genes highlighted in our genome-scale screen.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 44 Samples
FTP download: GEO (BW, CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128563/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA528105
Series		Accession: GSE128563	ID: 200128563

46. Re-programing chromatin with a bifunctional LSD1/HDAC inhibitor induces therapeutic differentiation in DIPG
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 30 Samples
FTP download: GEO (BED, BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110572/
Series		Accession: GSE110572	ID: 200110572

47. Distinct Roles of BET Family Members in ERα Enhancer Function and Gene Regulation in Breast Cancer Cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109572/
Series		Accession: GSE109572	ID: 200109572

48. Distinct Roles of BET Family Members in ERα Enhancer Function and Gene Regulation in Breast Cancer Cells [RNA-seq]
(Submitter supplied) Estrogen (E2)-dependent gene regulation mediated by estrogen receptor alpha (ERα) plays a mitogenic role in ER-positive breast cancer cells.  Although clinical applications of selective estrogen receptor modulators (SERMs), which directly interact with ERα to alter ERα activity, have been effective as a first line of treatment for breast cancer patients, a large subset of the patients will develop resistance after prolonged use of SERMs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109570/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431409
Series		Accession: GSE109570	ID: 200109570

49. Oncogenic zinc finger protein ZNF322A promotes lung cancer stemness through transcriptionally suppressing c-Myc expression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16288 8 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94657/
Series		Accession: GSE94657	ID: 200094657

50. Oncogenic zinc finger protein ZNF322A promotes lung cancer stemness through transcriptionally suppressing c-Myc expression [RNA-Seq]
(Submitter supplied) ZNF322A, a C2H2 zinc finger transcription factor, is an oncoprotein in lung cancer. However, the transcription mechanisms of ZNF322A in lung cancer stemness remain elusive. By integrating our chromatin immunoprecipitation-sequencing and RNA-sequencing datasets, we identified and validated transcriptional targets of ZNF322A, which significantly enriched in developmental processes. Indeed, overexpression of ZNF322A promoted self-renewal ability and increased stemness-related gene expressions in vitro and in vivo. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16288 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94537/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA371739
Series		Accession: GSE94537	ID: 200094537

51. Pharmacological Induction of a Progenitor State for the Efficient Expansion of Primary Human Hepatocytes
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87560/
Series		Accession: GSE87560	ID: 200087560

52. Pharmacological Induction of a Progenitor State for the Efficient Expansion of Primary Human Hepatocytes
(Submitter supplied) Transplantation of genetically corrected hepatocytes is an attractive alternative to liver transplantation but is hampered by the low amplification potential of these cells in vitro. Here, we describe a method for generating proliferative hepatic progenitor cells (iHPC) from human hepatocytes as an expandable cell source for liver therapy. Dedifferentiation of primary hepatocytes to iHPC was achieved in less than 7 days by culturing the cells in medium with a cocktail of growth factors and small molecules. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87559/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345196
Series		Accession: GSE87559	ID: 200087559

53. Pharmacological Induction of a Progenitor State for the Efficient Expansion of Primary Human Hepatocytes
(Submitter supplied) Transplantation of genetically corrected hepatocytes is an attractive alternative to liver transplantation but is hampered by the low amplification potential of these cells in vitro. Here, we describe a method for generating proliferative hepatic progenitor cells (iHPC) from human hepatocytes as an expandable cell source for liver therapy. Dedifferentiation of primary hepatocytes to iHPC was achieved in less than 7 days by culturing the cells in medium with a cocktail of growth factors and small molecules. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87558/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345193
Series		Accession: GSE87558	ID: 200087558

54. Multileveled reduction of p21 expression by Linc-ASEN represses cellular senescence
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (BED, BIGWIG, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128398/
Series		Accession: GSE128398	ID: 200128398

55. Multileveled reduction of p21 expression by Linc-ASEN represses cellular senescence [RNA-seq]
(Submitter supplied) Long noncoding RNAs regulating diverse cellular processes implicate in many diseases. Here, we report the identification of a novel long intergenic noncoding RNA, Linc-ASEN, expressed in prematurely senescent cells, that associates with UPF1 and represses cellular senescence by reducing p21 production transcriptionally and post-transcriptionally. The Linc-ASEN-UPF1 complex suppressed p21 transcription by recruiting Polycomb Repressive Complex 1 (PRC1) and PRC2 to the p21 locus, and thereby preventing binding of the transcriptional activator p53 on the p21 promoter. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128395/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA527316
Series		Accession: GSE128395	ID: 200128395

56. Therapeutic targeting of the pre-metastatic stage in human brain metastasis
(Submitter supplied) We have used our established brain metastasis initiating cell (BMIC) models and gene expression analyses to characterize pre-metastasis in human lung-to-brain metastases.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 36 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110495/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433863
Series		Accession: GSE110495	ID: 200110495

57. Subclonal cooperation drives metastasis through modulating local and systemic immune microenvironments
(Submitter supplied) Bulk RNA-Seq: Gene expression analysis of stromal and tumor fractions of primary and metastatic lesions of polyclonal and monoclonal origin. Primary tumor control samples consist of monoclonal Thy1.1 (no replicates), monoclonal parental (no replicates), monoclonal IL11 (duplicate), monoclonal FIGF (duplicate), and monoclonal CFP (duplicate). Primary polyclonal tumor samples consist of separated Thy 1.1 (duplicate), CFP (no replicates), IL11 (triplicate), and FIGF (triplicate). more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 121 Samples
FTP download: GEO (CSV, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109281/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA430336
Series		Accession: GSE109281	ID: 200109281

58. Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance
(Submitter supplied) RNAseq analysis upon KD of ZRF1 to prove that depletion of ZRF1 results in the acquisition of metastatic behavior and drug resistance via misregulation of cell death and cell survival related pathways in MCF7 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104675/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413470
Series		Accession: GSE104675	ID: 200104675

59. Napabucasin-mediated transcriptomic changes in human pancreatic cancer cell lines
(Submitter supplied) This study aimed to determine what genes are differentially expressed following 2 hours' treatment with napabucasin (BBI-608) alone or in combination with NQO1 depletion.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 23 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135352/
Series		Accession: GSE135352	ID: 200135352

60. Genome-wide maps of transcriptomic and epigenomic state in melanoma cell lines
(Submitter supplied) A mechanistic relationship between tumor epigenetic plasticity and nongenetic adaptive resistance to therapy is described, with MAPK inhibition of BRAF-mutant melanoma cells providing the model system. Upon inhibition, these largely melanocytic cells undergo reversible cell-state changes, ultimately yielding a drug-resistant mesenchymal-like phenotype. Epigenomic and transcriptomic kinetic studies, coupled with information theory and dynamic system modeling, revealed that, after just 3-days of treatment, RelA drives chromatin remodeling to establish an epigenetic program encoding long-term phenotype changes. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 45 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134459/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA555412
Series		Accession: GSE134459	ID: 200134459

61. TCF12 promotes the tumorigenesis and metastasis of hepatocellular carcinoma via upregulation of CXCR4 expression
(Submitter supplied) Stable ectopic TCF12 expression or knockdown in HCC cell lines was established by lentiviral infection. Then, MTT, colony formation, migration, invasion and HUVEC tube formation assays as well as an orthotopic xenograft model were used to investigate the biologic function of TCF12 in HCC cells in vitro and in vivo. Subsequently, RNA-Seq analysis was utilized to explore the target gene regulated by TCF12. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133553/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA551877
Series		Accession: GSE133553	ID: 200133553

62. RNA sequencing analysis after MK5 knockdown in LATS1/2-null RPE1 cells
(Submitter supplied) Transcriptional regulator YAP is activated in multiple human cancers and plays critical roles in tumor initiation, progression, metastasis, and drug resistance. However, therapeutic targeting of the Hippo-YAP pathway has been challenging due to its low druggability and limited knowledge of YAP regulation in cancer. Kinome siRNA library screening using an oncogenic YAP activation model identified the serine/threonine kinase MK5 as a positive regulator of YAP. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137816/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA573472
Series		Accession: GSE137816	ID: 200137816

63. Targeting the eIF4A dependent translation of KRAS and other oncoproteins in pancreatic cancer
(Submitter supplied) New and effective therapeutics are urgently needed for the treatment of pancreatic ductal adenocarcinoma (PDAC). The eIF4A/DDX2 RNA helicase drives translation of mRNAs with highly structured 5’UTRs. The natural compound silvestrol and synthetic analogues are potent and selective inhibitors of eIF4A1/2 that show promising activity in models of hematological malignancies. Here, we show silvestrol analogues have nanomolar activity against PDAC cell lines and organoids in vitro. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120159/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA491747
Series		Accession: GSE120159	ID: 200120159

64. Functional genomics of Caspase-3 deficiency or proficiency in MCF-7 cells or MDA-MB-231 tumors after docetaxel treatment
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL15520 12 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87227/
Series		Accession: GSE87227	ID: 200087227

65. Transcriptome analysis of Caspase-3 inhibited or not MDA-MB-231 tumors after docetaxel treatment
(Submitter supplied) We report that the inhibition of Caspase-3 reduced angiogenesis in vivo after docetaxel treatment
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87226/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA343939
Series		Accession: GSE87226	ID: 200087226

66. Transcriptome analysis of Caspase-3 deficient and proficient MCF-7 cells after docetaxel exposure
(Submitter supplied) We report that the presence of Caspase-3 induced expression of specific genes
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87225/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA344007
Series		Accession: GSE87225	ID: 200087225

67. Effect of high glucose on transcriptomic expression of cholangiocarcinoma cells
(Submitter supplied) This project was aimed to study the transciptomic profiles of cholangiocarcinoma cells cultured in different concentration of glucose. The established human cholangiocarcinoma cell line; KKU-213, and highly metastatic subline; KKU-213L5, were used. KKU-213 were cultured in either Dulbecco Modified Eagle's Medium (DMEM) with normal (5.6 mM) or high glucose (25 mM) and labeled as KKU-213NG or KKU-213HG according to thier cuture medium and KKU-213L5 was cultured in high glucose DMEM medium. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137803/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA573095
Series		Accession: GSE137803	ID: 200137803

68. IQGAP3 interacts with Rad17 to activate the MRN/ATM/Chk2 signaling and promote radioresistance in lung cancer
(Submitter supplied) IQ motif containing GTPase activating protein 3 (IQGAP3) has been implicated in diverse cellular processes including neuronal morphogenesis, cell proliferation and motility as well as epithelial-mesenchymal transition. However, its roles in DNA damage and repair remain to be clarified. Here, we demonstrate that IQGAP3 is frequently overproduced and predicts poor prognosis in lung cancer patients. Functionally, we provide evidence that depletion of IQGAP3 impairs tumorigenesis and overcomes radioresistance in lung cancer in vitro and in vivo. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137802/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA573096
Series		Accession: GSE137802	ID: 200137802

69. Proteasome Inhibition as a Therapeutic Approach in Atypical Teratoid/Rhabdoid Tumors
(Submitter supplied) Generation of fpkm lists for 6 cell lines
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137777/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA573051
Series		Accession: GSE137777	ID: 200137777

70. CREB5 promotes resistance to androgen-receptor antagonists and androgen deprivation in prostate cancer
(Submitter supplied) Inhibition of androgen-receptor (AR)signaling is the foundation of therapeutic regimens for advanced prostate cancers. However, nearly all patientsdevelop resistance and some never respond. To identify genes that mediate resistance to androgen ablation therapy, we performed an open reading frame (ORF) expression screen of17,255 ORFs and found that the transcription factorCREB5robustly conferred resistance to androgen deprivation and AR inhibition by enzalutamide. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL18573 28 Samples
FTP download: GEO (BW, CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137775/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA573060
Series		Accession: GSE137775	ID: 200137775

71. Phosphodiesterase 3A deficient in breast cancer cell
(Submitter supplied) Analysis of MDA-MB-231 breast tumor cell from knocking-down phosphodiesterase 3A (PDE3A), a cyclic nucleotide phosphodiesterase. Results provide insight into the role of PDE3A in breast tumor progression and metastasis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130569/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540659
Series		Accession: GSE130569	ID: 200130569

72. Transcriptome-wide analysis of wild-type and SRSF3-knockout glioma stem-like cells
(Submitter supplied) Purpose: The splicing factor SRSF3 is a member of serine- and arginine-rich proteins, which is frequently upregulated in various types of cancer. The aim of this study is to profile the alternative splicing (AS) events that were regulated by SRSF3 in glioma stem-like cells (GSCs). Methods: Total RNAs isolated from GSC83 and GSC528 cells with SRSF3-konckout (KO) or control (WT) were subjected to paired-end RNA-seq using the Illumina NextSeq 500 system according to the manufacturer's instruction. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130501/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540487
Series		Accession: GSE130501	ID: 200130501

73. FBP2 inhibits sarcoma progression by restraining mitochondrial biogenesis
(Submitter supplied) We show that expression of the gluconeogenic isozyme fructose-1,6-bisphosphatase 2 (FBP2) is silenced in a broad spectrum of soft tissue sarcoma (STS) subtypes, revealing an apparent common metabolic feature shared by diverse STS. Enforced FBP2 expression inhibits STS cell and tumor growth through two distinct mechanisms. First, cytosolic FBP2 antagonizes elevated glycolysis associated with the “Warburg effect”, thereby inhibiting sarcoma cell proliferation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137755/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA566448
Series		Accession: GSE137755	ID: 200137755

74. Identification of gene signature in ascitic fluid-isolated mesothelial cells from high grade serous ovarian cancer patients
(Submitter supplied) RNA-sequencing analysis was carried out on ascitic fluid-isolated mesothelial cells from ovarian cancer patients compared to control human peritoneal mesothelial cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 7 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120303/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA492459
Series		Accession: GSE120303	ID: 200120303

75. Enriched EWSR1 and EWS-FLI1 RNA-seq of HNRNPH1-silenced TC32 Ewing sarcoma and 293T human embryonic kidney cells.
(Submitter supplied) Identification of EWSR1 and EWS-FLI1 transcript variants associated with the silencing of HNRNPH1 in TC32 Ewing sarcoma and 293T human embryonic kidney (HEK-293T) cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119974/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490880
Series		Accession: GSE119974	ID: 200119974

76. Next Generation Sequencing to compare gene expression of PC-3M-Pro4 in cell culture and in zebrafish metastasis
(Submitter supplied) We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization.
Organism:	Danio rerio; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18413 GPL16791 GPL25625 9 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137629/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA566103
Series		Accession: GSE137629	ID: 200137629

77. Identification of PIKfyve kinase as a target in multiple myeloma
(Submitter supplied) The cellular cytotoxicity of APY0201, a PIKfyve inhibitor, against multiple myeloma was initially identified in an unbiased in vitro chemical library screen. Activity was confirmed in all 25 cell lines tested and 40% of 100 ex vivo patient derived primary samples, and positively correlated with samples harboring trisomies and inversely related to t(11;14). The broad anti- multiple myeloma activity of PIKfyve inhibitors was further demonstrated in confirmatory screens and showed the superior potency of APY0201 when compared to the PIKfyve inhibitors YM201636 and apilimod, with a mid-point EC50 at nanomolar concentrations respectively in 65%, 40%, and 5% of the tested cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 22 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134598/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA555832
Series		Accession: GSE134598	ID: 200134598

78. Discover of overlooked differentially expressed gene regions from single-cell RNA-seq data with neural stem cell derived from human induced pluripotent stem
(Submitter supplied) Single-cell RNA sequencing has enabled researchers to quantify the transcriptomes of individual cells, infer cell types, and investigate differential expression among cell types, which will lead to a better understanding of the regulatory mechanisms of cell states. Transcript diversity caused by phenomena such as aberrant splicing events have been revealed, and the differential expression of previously unannotated transcripts might be overlooked by annotation-based analyses. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 669 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125288/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515750
Series		Accession: GSE125288	ID: 200125288

79. Single cell RNA sequencing revealed a chemokine self-feeding of myeloma cells for extramedullary metastasis
(Submitter supplied) To determine the mechanisms of the initial extramedullary translocation of myeloma cells from bone marrow into peripheral blood.  We found that the clonal cPCs were more frequently detected by flowcytometry in extramedullary plasmacytoma patients and worsened their prognosis.  It is technically much easier to collect single cPCs using FACS than it is to perform EMP biopsy.  Combining imaging extramedullary plasmacytoma diagnosis and cPCs detection may be a promising strategy for prognostic stratification. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137545/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA565895
Series		Accession: GSE137545	ID: 200137545

80. Drivers of topoisomerase II poisoning mimic and complement cytotoxicity in AML cells
(Submitter supplied) Recently approved cancer drugs remain out-of-reach to most patients due to prohibitive costs and only few produce clinically meaningful benefits. An untapped alternative is to enhance the efficacy and safety of existing cancer treatments. We hypothesized that the response to topoisomerase II poisons, the most successful group of cancer drugs, can be improved by considering treatment-associated transcript levels, taken as surrogates for protein expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 66 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126895/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA523616
Series		Accession: GSE126895	ID: 200126895

81. RNA sequencing of wildtype-KRAS HKE3 (wtHKE3) and mutant-KRAS HKE3 (mtHKE3) colorectal cancer cell lines before and after stimulation with TGF-alpha
(Submitter supplied) RNA sequencing was performed on wtHKE3 and mtHKE3 colorectal cancer cell lines (obtained from Shirasawa [1]) before stimulation (timepoint 0) and at 15, 30, 60, 90 and 120 mins post-stimulation with transforming growth factor alpha (TGF-α) (0.01 µg/mL, Abcam). Three replicates were sequenced at each timepoint. [1] Tsunoda, Ishikura, Doi et al., Anticancer Res 2015, 35(8):4453-4459.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110649/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434191
Series		Accession: GSE110649	ID: 200110649

82. RNA sequencing of HCT116 and HKE3 colorectal cancer cell lines before and after stimulation with TGF-alpha
(Submitter supplied) RNA sequencing was performed on HCT116 and HKE3 colorectal cancer cell lines before stimulation and at 15, 30, 60, 90 and 120 mins post-stimulation with transforming growth factor alpha (TGF-α) (0.01 µg/mL, Abcam). Three replicates were sequenced at each time point.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE105nnn/GSE105094/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414626
Series		Accession: GSE105094	ID: 200105094

83. RNA-Seq reveals novel mechanistic targets of withaferin A (WA) in prostate cancer cells
(Submitter supplied) RNA-Seq analysis using WA-treated 22Rv1 human prostate cancer cells revealed upregulation and downregulation of 6993 and 6607 genes, respectively when compared to the vehicle-treated control. The pathways with significantly upregulated gene expression following WA treatment included mitogen-activated protein kinases, focal adhesion, endocytosis, and autophagy as revealed by KEGG and gene ontology analyses. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137519/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA565770
Series		Accession: GSE137519	ID: 200137519

84. Identification of a unique subtype of lung squamous cell carcinoma defined by SOX2 and a neural differentiation factor BRN2
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18573 51 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137461/
Series		Accession: GSE137461	ID: 200137461

85. Identification of a unique subtype of lung squamous cell carcinoma defined by SOX2 and a neural differentiation factor BRN2 [RNA-seq]
(Submitter supplied) Lineage-specific transcriptional regulators control differentiation states not only during normal development but also during cancer evolution. By investigating super-enhancer landscape of lung squamous cell carcinoma (LUSC), we identified a unique ‘neural’ subtype defined by Sox2 and a neural lineage factor Brn2. Robust protein-protein interaction and genomic co-occupancy of these factors indicated their transcriptional cooperation in this ‘neural’ LUSC in contrast to the cooperation of Sox2 and p63 in the classical LUSC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137460/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA565678
Series		Accession: GSE137460	ID: 200137460

86. Transcriptome data of uterine and ovarian carcinosarcoma tissues derived from patients in the Cancer Institute Hospital of Japanese Foundation for Cancer Research
(Submitter supplied) We performed RNA-seq experiments for total RNA of uterin and ovarian carcinosarcoma tissues.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 100 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128630/
Series		Accession: GSE128630	ID: 200128630

87. Effect of circPTPRM on the biological behaviors of hepatocellular carcinoma cells in vitro and its clinical significance.
(Submitter supplied) In this paper, a new circRNA was discovered by RNA sequencing, and its relationship with hepatocarcinoma proliferation, apoptosis, invasion and migration and clinical correlation of hepatocellular carcinoma were verified from different angles, providing a basis for further discussion on the mechanism of promoting the occurrence and development of hepatocellular carcinoma.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125469/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516450
Series		Accession: GSE125469	ID: 200125469

88. Cell differentiation grade determines distinct FOXA2 contributions to the cis-regulatory networks of pancreatic cancer cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing
Platforms: GPL18573 GPL9115 54 Samples
FTP download: GEO (NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120017/
Series		Accession: GSE120017	ID: 200120017

89. Cell differentiation grade determines distinct FOXA2 contributions to the cis-regulatory networks of pancreatic cancer cells [RNA-seq]
(Submitter supplied) Abnormal differentiation contributes to the spectrum of aberrant properties of tumor cells. Differentiation of both normal and tumor cells is controlled by regulatory networks enforced by transcription factors (TFs) involved in lineage specification. Among them, pioneer factors such as FOXA1/2, are able to bind and make accessible naïve chromatin, thus critically contributing to the establishment of gene regulatory networks. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119931/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490732
Series		Accession: GSE119931	ID: 200119931

90. ZRANB2 and SYF2 mediated splicing programs converging on ECT2 are involved in breast cancer cell resistance to doxorubicin
(Submitter supplied) We explored the regulation of alternative splicing in a cell model of breast cancer resistance to doxorubicin, and the impact of the depletion of two splicing factors (ZRANB2 and SYF2) in this context.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (BEDGRAPH, BW, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126365/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA521712
Series		Accession: GSE126365	ID: 200126365

91. RNA sequencing for lncRNA, miRNA and mRNA expression analysis in human laryngeal cancer
(Submitter supplied) Accumulating evidence indicates that long noncoding RNAs can interact with microRNAs to regulate target mRNAs through competing interactions. However, this mechanism remains largely unexplored in laryngeal squamous cell carcinoma. In this study, transcriptome-wide RNA sequencing in 3 pairs of laryngeal squamous cell carcinoma tissues and adjacent normal tissues was performed to investigate the expression profiles of lncRNAs, miRNAs and mRNAs.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT, XLS, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137308/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA565403
Series		Accession: GSE137308	ID: 200137308

92. Regulation of stem cell property and drug resistance of cancer cells by targeting transcriptional machinery via inhibition of neddylation
(Submitter supplied) MLN4924, also known as pevonedistat, is a small molecule inhibitor of NEDD8 activating enzyme (NAE), that inhibits the entire neddylation pathway. As the first-in-class neddylation inhibitor, MLN4924 is currently in Phase I/II clinical trials for anticancer application as a single agent or in combination with chemotherapeutic drugs. MLN4924 has shown impressive anticancer activity by inactivating Cullin-RING ligases (CRLs) to cause accumulation of tumor suppressor substrates. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134190/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA554253
Series		Accession: GSE134190	ID: 200134190

93. Differential gene expression between human colon cancers and the adjacent nomral colon tissues.
(Submitter supplied) We reported the gene expression profiles of 9 human colon cancer samples and their matching adjacent normal tissues.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137327/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA565188
Series		Accession: GSE137327	ID: 200137327

94. UMI-count modeling and differential expression analysis for single-cell RNA sequencing
(Submitter supplied) Single cell RNA-seq of the human alveolar rhabdomyosarcoma cell line Rh41.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (H5) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135564/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA559293
Series		Accession: GSE135564	ID: 200135564

95. A prostate cancer chromatin interaction map
(Submitter supplied) A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome  Prostate cancer (PCa) is the leading cancer among men in the United States. To understand gene regulation in 3D, chromatin interactions in prostate cancer cell is measured using in situ Hi-C. To better understand the impact of chromatin structure on regulation of the prostate cancer transcriptome, we developed high-resolution chromatin interaction maps in normal and prostate cancer cells using in situ Hi-C. more...
Organism:	Homo sapiens
Type:		Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 GPL21290 35 Samples
FTP download: GEO (BED, BROADPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118629/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486278
Series		Accession: GSE118629	ID: 200118629

96. Effects of ADAADi, an inhibitor of ATP-dependent chromatin remodeller, on human transcriptome
(Submitter supplied) Here we report the effects of Active DNA-dependent ATPase A Domain inhibitor (ADAADi) on human transcriptome
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137251/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA564932
Series		Accession: GSE137251	ID: 200137251

97. Patient-derived xenograft models of non-small cell lung cancer for evaluating targeted drug sensitivity and resistance
(Submitter supplied) Background: Patient-derived xenograft (PDX) models are a useful tool in cancer biology research. However, the number of lung cancer PDXs is limited Results: In the present study, we successfully established ten PDXs, including three adenocarcinoma (AD), six squamous cell carcinoma (SQ) and one large cell carcinoma (LA), from 30 patients with non-small cell lung cancer (NSCLC) (18 AD, 10 SQ, and 2 LA), mainly in SHO mice (Crlj:SHO-PrkdcscidHrhr). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130160/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA534119
Series		Accession: GSE130160	ID: 200130160

98. Identification of ZBTB7A cistrome and transcriptome profiles in VCaP prostate cancer cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123091/
Series		Accession: GSE123091	ID: 200123091

99. RNA-seq with knockdown ZBTB7A and NTC control
(Submitter supplied) Zinc finger and BTB domain containing transcription repressor ZBTB7A has been recently reported as a tumor suppressor who plays important functions to prevent the progression of prostate cancer. However, the chromatin activity of ZBTB7A in prostate cancer cells remain unclear. In order to identify the cistrome and transcriptome of ZBTB7A, we performed ZBTB7A ChIP-seq in VCaP cells and RNA-seq in VCaP cells transfected with siRNA targeting ZBTB7A or non-targeting control, respectively (cells were grown in full serum). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123090/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA507693
Series		Accession: GSE123090	ID: 200123090

100. Identification of FUBP1 as a long tail driver and widespread regulator of tumor suppressor and oncogene alternative splicing
(Submitter supplied) Comprehensive sequencing approaches have allowed for the identification of the most frequent contributors to cancer, known as drivers. They have also revealed a class of mutations in understudied, infrequently altered genes, referred to as “long tail” (LT) drivers. A key challenge has been to find clinically relevant LT drivers and understand how they cooperate to drive disease. Here, we identified Far Upstream Binding Protein 1 (FUBP1) as a LT driver using an in vivo CRISPR screen. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122416/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA505136
Series		Accession: GSE122416	ID: 200122416

101. The lncRNA NEAT1_1 is seemingly dispensable for normal tissue homeostasis and cancer cell growth
(Submitter supplied) NEAT1 is one of the most studied lncRNAs, in part because its silencing in mice causes defects in mammary gland development and corpus luteum formation and protects them from skin cancer development. Moreover, depleting NEAT1 in established cancer cell lines reduces growth and sensitizes cells to DNA damaging agents. However, NEAT1 produces two isoforms and because the short isoform, NEAT1_1, completely overlaps the 5' part of the long NEAT1_2 isoform, the respective contributions of each of the isoforms to these phenotypes has remained unclear. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 23 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137211/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA564816
Series		Accession: GSE137211	ID: 200137211

102. Effects of human adipose tissue-derived and umbilical cord tissue-derived mesenchymal stem cells in a dextran sulfate sodium-induced mouse model
(Submitter supplied) Background: Mesenchymal stem cells (MSCs) can be acquired from medical waste. MSCs are easily expanded and have multiple functions, including anti-inflammatory effects. We evaluated the effects of human adipose tissue-derived MSCs (AD-MSCs) and umbilical cord tissue-derived MSCs (UC-MSC) in a dextran sulfate sodium (DSS)-induced mouse model.    Methods: Human AD-MSCs and UC-MSCs (1 × 106 cells) were injected intravenously into a 7-day DSS-induced colitis model. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137173/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA564734
Series		Accession: GSE137173	ID: 200137173

103. Variant PRC2.1 and PRC2.2 co-operate to direct H3K27 methylations in ESCs
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Drosophila melanogaster; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL25537 GPL19415 GPL19057 79 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127121/
Series		Accession: GSE127121	ID: 200127121

104. TAF1 is critical for AE driven leukemogenesis [RNA-seq]
(Submitter supplied) TAF1 is essential for AE driven leukemogenesis. Depletion of TAF1 impairs the recruitment of AE to its target genes, interfering with its control of gene expression. The bromodomains of TAF1 associate with K43 acetylated AE and this association plays a role in the proliferation of AE expressing AML cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 19 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115121/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA473831
Series		Accession: GSE115121	ID: 200115121

105. Dual role of CSL (RBP-Jk) and NOTCH1 in cancer-associated fibroblast genome stability and expansion [RNA-seq]
(Submitter supplied) Genomic instability is a hallmark of cancer. Whether or not it also occurs in cancer-associated fibroblasts (CAFs) is a question of importance for the cancer/stromal cell co-evolution process. We find that DNA damage, telomere shortening and chromosome fusions occur at early times of CAF activation, as triggered by silencing of the CSL/RBP-J-κ gene in primary human dermal fibroblasts (HDFs) from multiple individuals. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113542/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA451482
Series		Accession: GSE113542	ID: 200113542

106. TAF1 is critical for AE driven leukemogenesis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18573 44 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100446/
Series		Accession: GSE100446	ID: 200100446

107. Transcriptome analysis reveals malignant and hypoxic signature of glioblastoma
(Submitter supplied) Purpose:Glioblastoma (GBM) is the most common primary brain tumor in adults with poor prognosis and short medial survival after therapy. we have utilized U87-MG cell line as a human GBM cell model and human brain HEB cell line as non-neoplastic brain cell cultured in normoxia and 1% O2 hypoxia for transcriptional profiling to gain further insight into the molecular underpinnings that maintained the properties of GBM andclarify the molecular mechanism of hypoxia resistance of GBM. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77307/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310001
Series		Accession: GSE77307	ID: 200077307

108. Single-cell transcriptome analysis reveals gene signatures associated with T-cell persistence following adoptive cell therapy
(Submitter supplied) A patient (4095) with metastatic colorectal cancer was treated with polyclonal tumor infiltrating lymphocytes (TILs) targeting the KRAS(G12D) hotspot mutation. Three dominant clonotypes  specifically recognizing KRAS(G12D) epitopes were identified, but we found that only two clonotypes persisted 40 days after TIL treatment. Because of these findings, in this study, we utilized a 10X system to perform single-cell TCR/transcriptome analysis for the TILs isolated from this patient, together with 4 additional TILs isolated from 4 patients (4007, 4069, 4071, 4081) treated within 5-month window. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL21697 32 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136394/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA562473
Series		Accession: GSE136394	ID: 200136394

109. The Single Cell Transcriptomic Landscape of Early Human Diabetic Nephropathy
(Submitter supplied) We report the early transcriptional changes in human diabetic nephropathy by single nucleus RNA sequencing
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 6 Samples
FTP download: GEO (RDS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131882/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA545232
Series		Accession: GSE131882	ID: 200131882

110. AML subtype is a major determinant of the association between prognostic gene expression signatures and their clinical significance.
(Submitter supplied) Relapse in acute myeloid leukemia (AML) may result from variable genetic origins or convergence on common biological processes. Exploiting the specificity and sensitivity of regulatory DNA, we analyze patient samples of multiple clinical outcomes covering various AML molecular subtypes. We uncover regulatory variation between patients translating into a transcriptional signature that predicts relapse risk. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 43 Samples
FTP download: GEO (BW, NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117994/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483951
Series		Accession: GSE117994	ID: 200117994

111. MicroRNA-194 promotes lineage plasticity in advanced prostate cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 14 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137072/
Series		Accession: GSE137072	ID: 200137072

112. MicroRNA-194 promotes lineage plasticity in advanced prostate cancer [HITS-CLIP]
(Submitter supplied) MicroRNA-194 (miR-194) promotes prostate cancer metastasis, but the precise molecular mechanisms by which it achieves this are unknown. Here, by integrating Argonaute high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (Ago-HITS-CLIP) with RNA sequencing and exon-intron split analysis, we defined a 163-gene miR-194 “targetome” in prostate cancer. These target genes were predominantly down-regulated through canonical 3’UTR recognition sites and were enriched within pathways involved in cytoskeletal organisation and cell movement. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (BIGWIG, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137071/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA564505
Series		Accession: GSE137071	ID: 200137071

113. MicroRNA-194 promotes lineage plasticity in advanced prostate cancer [RNA-Seq]
(Submitter supplied) MicroRNA-194 (miR-194) promotes prostate cancer metastasis, but the precise molecular mechanisms by which it achieves this are unknown. Here, by integrating Argonaute high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (Ago-HITS-CLIP) with RNA sequencing and exon-intron split analysis, we defined a 163-gene miR-194 “targetome” in prostate cancer. These target genes were predominantly down-regulated through canonical 3’UTR recognition sites and were enriched within pathways involved in cytoskeletal organisation and cell movement. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137070/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA564504
Series		Accession: GSE137070	ID: 200137070

114. A single cell reference map for human blood and tissue T cell activation
(Submitter supplied) Human T cells coordinate adaptive immunity by localization in diverse tissue sites, though blood T cells are the most readily studied.  We investigated the functional responses of T cells isolated from human lungs (LG), lymph nodes (LN), bone marrow (BM), and blood to TCR-stimulation using single-cell RNA-seq. We defined cellular states for resting T cells including signatures that differentiate tissue and blood T cells and employed new factorization methods to identify activation states conserved across tissues, including an IFN-response activation state in CD4+T cells and distinct effector states specific to CD8+T cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126030/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA520832
Series		Accession: GSE126030	ID: 200126030

115. Stranded RNA-seq were performed on total RNA following ribosomal RNAs depletion (Ribo-zero removal kit, illumina) for 3 brain , 8 IDHwt and 5 IDHmut glioma samples.
(Submitter supplied) Aberrant DNA methylation is a well-defined feature of cancer cells that is commonly associated to transcriptional alteration. Nonetheless, a primary role of this defect in genome-wide cancer-associated gene misregulation is still being questioned.  Here, we used adult glioma, a widespread type of brain tumor, to evaluate the relative contribution of DNA methylation-dependent and -independent mechanisms on transcriptional alteration at CpG-island/promoter-associated genes in cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123892/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510124
Series		Accession: GSE123892	ID: 200123892

116. TGF-b-activated LncRNA LINC00115 is a critical regulator for glioma stem-like cell tumorigenicity
(Submitter supplied) Long non-coding RNAs (lncRNAs) are critical regulators in cancer. However, the involvement of lncRNAs in TGF-beta-regulated tumorigenicity is still unclear. Here we identify TGF-beta-activated lncRNA LINC00115 as a critical regulator in glioma stem-like cell (GSC) self-renewal and tumorigenicity. LINC00115 is upregulated by TGF-beta, acts as a miRNA sponge and upregulates ZEB1 by competitively binding miR-200s, thereby enhancing ZEB1 signaling and GSC self-renewal.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20795 GPL16791 14 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134595/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA555792
Series		Accession: GSE134595	ID: 200134595

117. Differential modulation of the androgen receptor for prostate cancer therapy depends on the DNA response element
(Submitter supplied) Doxorubicin Treated LNCaP cells RNA-sequencing, and AR and TBP Chromatin immunoprecipitation sequencing
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 38 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137056/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA564340
Series		Accession: GSE137056	ID: 200137056

118. Elucidating the microRNA-203 specific biological processes in glioblastoma cells from comprehensive high-throughput RNA-sequencing transcriptome profiling
(Submitter supplied) We report the application of high-throughput RNA-sequencing Profile of miR-203 expressing glioma U251 cells. Glioblastoma (GBM) is the most common primary malignant intracranial adult brain tumor. Allelic deletion on chromosome 14q plays an essential role in GBM pathogenesis, and this chromosome 14q site was thought to harbor multiple tumor suppressor genes associated with GBM, a region that also encodes microRNA-203 (miR-203). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119711/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490091
Series		Accession: GSE119711	ID: 200119711

119. Identification of miRNA-mRNA regulatory network for Human Atrial Aging [mRNA]
(Submitter supplied) We report an integrative analysis of miRNA-seq and mRNA-seq to identify miRNAs, genes, and miRNA-mRNA interactions for human atrial aging (AA). We found that seven miRNAs (4 upregulation and 3 downregulation) and 42 genes (23 upregulation and 19 downregulation) show differential expression between older samples and younger samples in human right atrial tissues. Pearson correlation analysis identified 114 pairs of putative miRNA-mRNA interactions for AA. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136928/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA564076
Series		Accession: GSE136928	ID: 200136928

120. Human bladder cancer cell line mRNA-seq
(Submitter supplied) Circular RNAs (circRNAs) have been increasingly indicated to be important participants in the development and progression of various malignant tumors. Our previous studies found that hundreds of circRNAs were aberrantly expressed in bladder cancer (BC) by high-throughput sequencing and we have confirmed that the downregulated circRNAs circHIPK3, BCRC3 and circNR3C1 played inhibitory roles in BC progression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136919/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA564038
Series		Accession: GSE136919	ID: 200136919

121. RNAseq analysis of ESRP regulated splicing events in prostate cancer
(Submitter supplied) Progression of prostate cancer -the most frequent cancer in men- is driven by androgen steroid hormones, and delayed by androgen deprivation therapy (ADT). Androgens control transcription in prostate cancer cells by stimulating androgen receptor (AR) activity, but also control pre-mRNA splicing through less clear mechanisms. Here we examine whether androgens regulate splicing through AR-mediated transcriptional control of splicing regulator proteins. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129540/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA531685
Series		Accession: GSE129540	ID: 200129540

122. RNA-Seq analysis miR-455-3p overexpression effect on breast cancer cell line
(Submitter supplied) MiR-455-3p has been reported to suppress the expression of ROCK2, HOXB5, hTERT, and RUNX2, which are involved in multiple biological processes including renal fibrosis, chondrogenic development and differentiation, Alzheimer’s disease, preeclampsia, and tumorigenesis. Here, we showed that miR-455-3p broadly inhibited TGF-beta-induced EMT by repressing the expression of Smad2, ZEB1, and HDAC2 in breast cancer cells, and that miR-455-3p loss-of-function promotes the acquisition of cell invasive properties and the ability to metastasize. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129146/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA530241
Series		Accession: GSE129146	ID: 200129146

123. The impact of stanniocalcin 1 on the transcriptome of human cord blood stem/progenitors
(Submitter supplied) Purpose: Stanniocalcin 1 (STC1) is a secreted glycoprotein expressed in mesenchymal stroma cells (MSCs). STC1 expression is upregulated in response to acute myeloid leukemia (AML) co-culture. Recombinant STC1 has proliferation limiting effects on human hematopoietic stem/progenitors cells (HSPCs) and facilitiates the preservation of HSCs ex vivo. We hope to gain insight into the mechanism by exploring the transcriptome of stem/progenitors exposed to STC1.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 18 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136884/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA563915
Series		Accession: GSE136884	ID: 200136884

124. Conversion of Sox2-Dependent Merkel Cell Carcinoma to a Differentiated Neuron-like Phenotype by T Antigen Inhibition
(Submitter supplied) Keratinocyte-cocultured Merkel cell carcinoma cell line (MCC) CVG-1 cells transduced with contorl shRNA (shCtrl) and viral T antigen targeting shRNA (shpanT) were sequenced using the 10x Genomics platform in order to analyze transcriptional changes associated with MCC cancer cell differentiation into neuron-like cells on a single cell level.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (H5) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136867/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA563893
Series		Accession: GSE136867	ID: 200136867

125. Discovery and verification of liver cancer marker genes and variable scission based on second-generation sequencing data analysis
(Submitter supplied) The RNA-seq technique was used to sequence the liver cancer tissues and paracancerous tissues of 6 clinical patients, aiming to find differentially expressed genes and transcripts, and to verify the expression level and function of the expression. To improve the accuracy of gene discovery, we used two methods to analyze the sequencing data.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136846/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA563853
Series		Accession: GSE136846	ID: 200136846

126. DJ-1 is dispensable for human stem cell homeostasis
(Submitter supplied) our data showed that the absence of DJ-1 had no adverse effects on proliferation, differentiation, and oxidative stress responses of human stem cells such as hNSCs and hMSCs as well as hVECs, suggesting that loss of DJ-1 function alone is insufficient to disrupt the homeostasis of these human cells. In addition, we found that CHCHD2 was upregulated upon DJ-1 deficiency, which may account for the absence of severe phenotypes in various types of DJ-1-deficient cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136834/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA563836
Series		Accession: GSE136834	ID: 200136834

127. Impact of GDF15 expression of ovarian cancer cell on stroma and Cisplatin responses
(Submitter supplied) We report the RNAseq data from xenografts mouse models generated from human ovarian cancer cell lines A2780 with GDF15 expression knockdown with shRNA
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132610/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA548552
Series		Accession: GSE132610	ID: 200132610

128. Distinct imprinting signatures and biased differentiation of human androgenetic and parthenogenetic embryonic stem cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by array
Platforms: GPL18573 GPL16791 GPL13534 64 Samples
FTP download: GEO (IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114679/
Series		Accession: GSE114679	ID: 200114679

129. Distinct imprinting signatures and biased differentiation of human androgenetic and parthenogenetic embryonic stem cells [RNA-Seq II]
(Submitter supplied) Genomic imprinting is an epigenetic mechanism that results in parent-of-origin monoallelic expression of specific genes, which precludes uniparental development and underlies various diseases. Here, we explored molecular and developmental aspects of imprinting in humans by generating exclusively paternal human androgenetic embryonic stem cells (aESCs) and comparing them with exclusively maternal parthenogenetic ESCs (pESCs) and bi-parental ESCs, establishing a pluripotent cell system of distinct parental backgrounds. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 48 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114677/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472150
Series		Accession: GSE114677	ID: 200114677

130. Non-functioning pituitary adenomas AmpliSeq data
(Submitter supplied) This dataset contains high throughput sequencing data from Non-functioning pituitary adenomas (NFPAs) together with associated control sections of healthy pituitary which was obtained from formalin-fixed paraffin embeded samples. All of the samles come from patients of Maria Sklodowska-Curie Memorial Cancer Center in Warsaw. All the samples were sequenced using Ion Torrent technology in Maria Sklodwoska-Curie Memorial Cancer Center in Warsaw. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 46 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136781/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA563652
Series		Accession: GSE136781	ID: 200136781

131. Endogenous retroviruses are a source of oncogenic enhancers in acute myeloid leukemia
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18573 32 Samples
FTP download: GEO (BROADPEAK, BW, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136764/
Series		Accession: GSE136764	ID: 200136764

132. Endogenous retroviruses are a source of oncogenic enhancers in acute myeloid leukemia [RNA-Seq]
(Submitter supplied) Endogenous retroviruses (ERVs) and other transposons can act as tissue-specific regulators of gene expression in cis, with potential to affect biological processes. In cancer, epigenetic alterations and transcription factor misregulation may uncover the regulatory potential of typically repressed ERVs, which could contribute to tumour evolution and progression. Here, we asked whether transposons help to rewire oncogenic transcriptional circuits in acute myeloid leukaemia (AML). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 10 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136763/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA563622
Series		Accession: GSE136763	ID: 200136763

133. RNA-seq analysis of gene expression profile in PTEN WT and KO LN229 glioblastoma multiforme (GBM) Xenograft tumor Transcriptomes
(Submitter supplied) The goal of this study is to compare gene expression profiles of PTEN WT and KO GBM cells when they are growing in vivo. Isogenic PTEN WT or KO LN229 GBM cells were subcutaneously implanted into Balb/c nude mice (two in each group) to form tumor. At the 30th day tumors were harvested and total RNA was isolated. RNA-seq analysis was performed to examine the differential express pattern of the two type of xenografts.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136738/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA563550
Series		Accession: GSE136738	ID: 200136738

134. Hypoxic transcriptomic signature of A549 cells (RNA-Seq)
(Submitter supplied) To assess the transcriptomic response of the LUAD cell line A549 to hypoxia, cells were exposed to 1% (Hx) or 21% O2 (Nx) during 24 hours. Two µg of total RNAs were depleted from ribosomal RNA with the Ribozero kit (epicenter), libraries were generated with the NEBNext Small RNA Library Prep Set for SOLiD and sequenced on SOLiD 5500XL (Life Technologies) with single-end 50bp reads. Reads were aligned to the human genome release hg19 with the LifeScope software v2.5.1 (Life Technologies) using whole transcriptome pipeline for RNA‐seq libraries with default parameters.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16558 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117048/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480905
Series		Accession: GSE117048	ID: 200117048

135. RNA-seq profiling of parental and NLUCAT1-deleted A549 cells under hypoxia
(Submitter supplied) Parental or NLUCAT1 CRISPR/Cas9-deleted A549 clones (WT A549 Hx, n = 1 clone; DEL A549 Hx, n = 1 clone) were exposed to hypoxia (Hx) at 1% O2 for 24 hours. Libraries were generated from 500 ng of total RNAs using TruSeq Stranded Total RNA kit with Ribo-Zero (Illumina) and sequenced on a NextSeq500 sequencer (Illumina) with 2x75bp paired-end chemistry. Reads were aligned to the human genome release hg19 using STAR v2.4.0a with default parameters.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117044/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480897
Series		Accession: GSE117044	ID: 200117044

136. Target Gene Repression Based on Dismissal of Polymerase II from Estrogen Receptor Trans-bound Enhancers Is Associated With Clinical Outcome in Human Breast Cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.  Keywords: Genome binding/occupancy profiling by high throughput sequencing
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 48 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73958/
Series		Accession: GSE73958	ID: 200073958

137. Target Gene Repression Based on Dismissal of Polymerase II from Estrogen Receptor Trans-bound Enhancers Is Associated With Clinical Outcome in Human Breast Cancer [GRO-seq]
(Submitter supplied) We find that 17-β-estradiol (E2)-bound estrogen receptor α (ERα) is bound in trans to a cohort of FOXA1-dependent, constitutively activate enhancers, inactivating these enhancers by decommissioning/removing enhancer Polymerase II (Pol II), despite recruitment of coactivators. This is based on the surprising recruitment by the ERα DNA binding domain of the histone demethylase, KDM2A, which, functioning independently of its demethylase function. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 14 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73957/
Series		Accession: GSE73957	ID: 200073957

138. NSD2 overexpression links drives clustered chromatin and transcriptional changes in a subset of insulated domains   of insulated domains
(Submitter supplied) We analyzed the impact of NSD2 overexpression on 3D genome reorganization and gene expression in multiple myeloma cell lines
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 48 Samples
FTP download: GEO (BED, BEDGRAPH, BW, HIC, NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131651/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA544287
Series		Accession: GSE131651	ID: 200131651

139. Molecular determinants for enzalutamide-induced transcription in prostate cancer
(Submitter supplied) Enzalutamide, a second-generation androgen receptor (AR) antagonist, has demonstrated clinical benefit in men with prostate cancer. However, it only provides a temporary response and modest increase in survival, indicating a rapid evolution of resistance. Previous studies suggest  that enzalutamide may function as a partial transcriptional agonist, but the underlying mechanisms for enzalutamide-induced transcription remain poorly understood. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125014/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA514909
Series		Accession: GSE125014	ID: 200125014

140. Characterization of an Immortalized Human Small Airway Basal Stem/Progenitor Cell Line with Airway Region-specific Differentiation Capacity [RNA-Seq]
(Submitter supplied) The pathology of chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis and the majority of lung cancers involve the small airway epithelium (SAE), the single continuous layer of cells lining the airways ≥6th generations. The basal cells (BC) are the stem/progenitor cells of the SAE, responsible for the differentiation into intermediate cells and ciliated, club and mucous differentiated cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124258/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA511423
Series		Accession: GSE124258	ID: 200124258

141. Interaction between oncogenic FREM2 with IL-1β signaling contributes to esophageal squamous cell carcinoma progression
(Submitter supplied) Inflammatory signals can promote tumorigenesis. The pro-inflammatory cytokine interleukin (IL)-1β is overexpressed in many types of tumor; however, it is unclear whether it directly interacted with oncogenes in esophageal squamous cell carcinoma. In this study, we performed RNA sequencing to identify tumorgenesis and recurrence-related factors in ESCC and identified FRAS1-related extracellular matrix protein (FREM)2 as a candidate oncogene. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119436/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489250
Series		Accession: GSE119436	ID: 200119436

142. The nuclear hypoxia-regulated NLUCAT1 long non-coding RNA contributes to an aggressive phenotype in lung adenocarcinoma through regulation of oxidative stress
(Submitter supplied) Lung cancer is the leading cause of cancer death worldwide, with poor prognosis and a high rate of recurrence despite early surgical removal. Hypoxic regions within tumors represent sources of aggressiveness and resistance to therapy. While long non-coding RNAs (lncRNAs) are increasingly recognized as major gene expression regulators, their regulation and function following hypoxic stress are still largely unexplored. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL17077 GPL16558 GPL18573 88 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117049/
Series		Accession: GSE117049	ID: 200117049

143. Endogenous interaction profiling identifies DDX5 as an oncogenic coactivator of transcription factor Fra-1
(Submitter supplied) Fra-1, a member of the activator protein 1 (AP-1) family, is overexpressed in triple-negative breast cancer (TNBC) and plays crucial roles in tumor growth. Here we report the identification of 118 proteins interacting with endogenous chromatin-bound Fra-1 in TNBC cells, highlighting DDX5 as the most enriched Fra-1-interacting protein. DDX5, a previously unrecognized protein in the Fra-1 transcriptional network, shows extensive overlap with Fra-1 cistrome and transcriptome that are highly associated with the TNBC cell growth. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL11154 13 Samples
FTP download: GEO (GTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112963/
Series		Accession: GSE112963	ID: 200112963

144. Endogenous interaction profiling identifies DDX5 as an oncogenic coactivator of transcription factor Fra-1 [RNA-seq]
(Submitter supplied) Fra-1, a member of the activator protein 1 (AP-1) family, is overexpressed in triple-negative breast cancer (TNBC) and plays crucial roles in tumor progression. However, a systematic analysis of the composition of the Fra-1 protein network specifically on chromatin is still missing. Here we performed endogenous purification of Fra-1 transcriptional complex under ChIP conditions, followed by mass spectrometry, to identify chromatin-bound partners of Fra-1 in TNBC cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112962/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA449623
Series		Accession: GSE112962	ID: 200112962

145. Dynamic incorporation of histone H3 variants into chromatin is essential for acquisition of aggressive traits and metastatic colonization 
(Submitter supplied) Carcinomas can acquire metastatic potential by undergoing a cellular program referred to as epithelial-to-mesenchymal transition (EMT). During EMT, the genome undergoes major epigenetic changes required for the expression of genes that promote cell motility, invasiveness, and survival under stress. While recent data point to a crucial role of chromatin remodeling in this process, little is known about the nature of this remodeling and the signals that trigger it. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119030/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487797
Series		Accession: GSE119030	ID: 200119030

146. A novel reprogramming strategy to generate functionally competent human hepatocytes
(Submitter supplied) Cell fate can be directly converted between differentiated cells by lineage reprogramming, thus generating multiple cell types across developmental lineages. However, lineage reprogramming is hindered by incomplete cell-fate conversion with residual initial cell identity and partial functions compared with the native counterparts. Here, we develop a high-fidelity reprogramming strategy, by mimicking the natural cell-fate changing route, thus permitting the production of functionally competent human hepatocytes from another cell type. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL20301 GPL16791 47 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112330/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA445694
Series		Accession: GSE112330	ID: 200112330

147. Effect of Omomyc treatment on MYC mediated transcription
(Submitter supplied) Purpose: Identify MYC sensitive enes that are affected by treatment with Omomyc
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131075/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA542602
Series		Accession: GSE131075	ID: 200131075

148. Single cell RNA-seq profiling of two bladder cancer specimen
(Submitter supplied) To explore the heterogeneity of stromal compartment of bladder cancer, we performed scRNAseq on two muscle-invasive bladder cancer specimens
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130001/
Series		Accession: GSE130001	ID: 200130001

149. Gene expression profiling in  Osteosarcomas
(Submitter supplied) To explore whether KSHV infection is a risk factor for osteosarcoma development in ethnic Uyghur population. Sarcoma specimens including tumor, adjacent normal tissues and paired blood samples were obtained from several osteosarcoma patients of Xinjiang China. Then, osteosarcoma clinical samples were subjected to analysis for the presence of the KSHV genome and proteins. Gene expression profiles of these osteosarcomas were analyzed to reveal the pathogenesis of KSHV-positive and -negative osteosarcomas.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126209/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA518013
Series		Accession: GSE126209	ID: 200126209

150. LSD1-RCOR2 binding and LSD1 and BRD9 transcriptome analysis in Merkel cell carcinoma cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 58 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124864/
Series		Accession: GSE124864	ID: 200124864

151. LSD1 and BRD9 transcriptome analysis in the MKL-1 Merkel cell carcinoma (MCC) cell line
(Submitter supplied) Merkel cell carcinoma (MCC) is an aggressive neuroendocrine cancer of the skin, caused by either excessive UV damage or integration of the Merkel cell polyomavirus (MCV) genome. Here, we report that virally encoded MCV small T antigen (ST) establishes dependence on the LSD1 transcriptional repressor. Inhibition of LSD1 reduces growth of MCV-positive MCC and suppresses ST’s transformation capacity in vitro and in vivo. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124861/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA514038
Series		Accession: GSE124861	ID: 200124861

152. LSD1 transcriptome analysis in Merkel cell carcinoma (MCC) cell lines
(Submitter supplied) Merkel cell carcinoma (MCC) is an aggressive neuroendocrine cancer of the skin, caused by either excessive UV damage or integration of the Merkel cell polyomavirus (MCV) genome. Here, we report that virally encoded MCV small T antigen (ST) establishes dependence on the LSD1 transcriptional repressor. Inhibition of LSD1 reduces growth of MCV-positive MCC and suppresses ST’s transformation capacity in vitro and in vivo. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 42 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124857/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA514037
Series		Accession: GSE124857	ID: 200124857

153. RNA-Seq of patient derived osteosarcoma xenograft samples
(Submitter supplied) Observing the gene expression of  ATRX, DAXX, H3F3A, SMARCAL1, SLX4IP and TERT in 7 patient derived osteosarcoma xenograft samples (Houghton et al., 2007) which are using the Alternative Lengthening of Telomere (ALT) pathway.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 60 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124768/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA513353
Series		Accession: GSE124768	ID: 200124768

154. Robust, long-term culture of endoderm derived hepatic organoids (eHEPOs) for disease modeling
(Submitter supplied) Many liver pathologies ranging from cancer to genetic metabolic diseases are amenable to cellular replacement therapies. One of the main difficulties associated with cellular therapy approaches is the generation and expansion of mature autologous hepatocytes. The ability to derive patient-specific induced pluripotent stem cells (iPSCs) have solved the problem of generating autologous cells but differentiation and expansion of mature hepatocytes remain a challenge. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 24 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120145/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA491723
Series		Accession: GSE120145	ID: 200120145

155. Expression Analysis of dic(1;7)(q10;p10) in Myelodysplastic Syndromes (MDS) compared to control cohort and therapy-related Myeloid Neoplasms (t-MN)
(Submitter supplied) The unbalanced translocation t(1;7)(q10;p10), generating 1q trisomy and  7q monosomy, is due to centromere-centromere juxtaposition. This dicentric chromosome is a recurrent change in myelodysplastic syndromes (MDS), with half the cases arising after chemo/radio-therapy. To date, given the absence of genes within the centromeric regions, no specific molecular events have been identified in this cytogenetic subgroup. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118476/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485753
Series		Accession: GSE118476	ID: 200118476

156. LEDGF and HDGF2, histone H3K36 methyl-binding proteins that assist RNA polymerase II transcription through nucleosomes
(Submitter supplied) FACT (facilitates chromatin transcription) is a protein complex that allows RNAPII to overcome the nucleosome-induced barrier to transcription.  While abundant in stem cells and many cancer cells, FACT it is not very abundant in most tissues.  Therefore, we screened for additional factors that might replace FACT in such tissues.  Here we report the identification of two such proteins, LEDGF and HDGF2, each containing two HMGA-like AT-hooks and a PWWP methyl-lysine reading domain known to bind to H3K36me2 and H3K36me3. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL17021 64 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117155/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481318
Series		Accession: GSE117155	ID: 200117155

157. Transcriptomics-based drug repurposing approach identifies novel drugs against sorafenib-resistant hepatocellular carcinoma
(Submitter supplied) Hepatocellular carcinoma (HCC) is frequently diagnosed in patients with late-stage disease who are ineligible for curative surgical therapies. Furthermore, the majority of patients become resistant to sorafenib. Recently, computational methods for drug repurposing have shown great promise to accelerate the discovery of new uses for existing drugs. In order to identify novel drugs for use against sorafenib resistant (SR)-HCC, we employed a transcriptomics-based drug repurposing method termed connectivity mapping. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113005/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA449722
Series		Accession: GSE113005	ID: 200113005

158. Retinoid induced differentiation of NB4 APL leukemic cells
(Submitter supplied) We report the use of RNAseq to determine genomewide transcriptional changes induced by all-trans retinoic acid differentiation of NB4 acute promyelocytic leukemia (APL) cells.  
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53259/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA231462
Series		Accession: GSE53259	ID: 200053259

159. The role of TFEB in retinoid induced differentiation of NB4 APL leukemic cells (shTFEB)
(Submitter supplied) We report the use of RNAseq to determine the role of the TFEB transcription factor in all-trans retinoic acid induced differentiation of NB4 acute promyelocytic leukemia (APL) cells. We used lentiviral mediated shRNA approaches to functionally deplete TFEB in NB4 cells and compared the transcriptomes of wild type, scramble control shRNA and  shTFEB knockdown cells treated with ethanol (control) versus all-trans retinoic acid for 72 hours.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53258/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA231463
Series		Accession: GSE53258	ID: 200053258

160. YTHDF1 Amplifies Wnt/β-Catenin Signaling to Promote Intestinal Stemness
(Submitter supplied) Wnt/β-catenin signaling is essential for intestinal stem cell homeostasis and aberrant activation of this signaling leads to tumorigenesis. Here we report a function of YTHDF1, an mRNA m6A reader, in mediating β-catenin hyperactivation. Wnt signaling promotes YTHDF1 expression at the translational level. YTHDF1 is dispensable for normal intestinal development in mice while essential for intestinal regeneration. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL20795 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136664/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA563001
Series		Accession: GSE136664	ID: 200136664

161. The role of PHF19 in promoting H3K27me3 deposition in multiple myeloma (RNA-Seq)
(Submitter supplied) Dysregulation of Polycomb Repressive Complex 2 (PRC2) promotes oncogenesis partly through its enzymatic function for inducing tri-methylation of histone H3 lysine 27 (H3K27me3). However, it remains to be determined how PRC2 activity is regulated in normal and diseased settings. We here report a PRC2-associated cofactor, PHD finger protein 19 (PHF19, also known as Polycomb-like 3), as a crucial mediator of tumorigenicity in multiple myeloma (MM). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136410/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA562526
Series		Accession: GSE136410	ID: 200136410

162. The role of PHF19 in promoting H3K27me3 deposition in multiple myeloma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 13 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135895/
Series		Accession: GSE135895	ID: 200135895

163. Comprehensive landscape of active deubiquitinating enzymes profiled by advanced chemoproteomics
(Submitter supplied) Enzymes that bind and process ubiquitin, a small 76 amino acid protein, have been recognized as pharmacological targets in oncology, immunological disorders and neurodegeneration. Mass spectrometry technology has now reached the capacity to cover the proteome with enough depth to interrogate entire biochemical pathways including those that contain DUBs and E3 ligase substrates. We have recently characterized the breast cancer cell (MCF7) deep proteome by detecting and quantifying ~10,000 proteins, and within this data set, we can detect endogenous expression of 65 deubiquitylating enzymes (DUBs), whereas matching transcriptomics detected 78 DUB mRNAs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 1 Sample
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134954/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA556874
Series		Accession: GSE134954	ID: 200134954

164. Combined inhibition of STAT3 and DNA repair in palbociclib-resistant ER-positive breast cancer
(Submitter supplied) The results from our study have identified two clinically relevant, divergent and druggable pathways (DNA repair and STAT3) that can be targeted in combination to effectively combat drug resistance. We also found that the same pathways that were deregulated in palbociclib-resistant cells were also altered in tumor samples obtained from patients who progressed while on palbociclib and endocrine therapy
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 7 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128056/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA526217
Series		Accession: GSE128056	ID: 200128056

165. Translocation driven high expression of NOTCH2 in glomus tumors of the upper digestive tract
(Submitter supplied) Glomus tumors (GT) are perivascular tumors mostly occurring in the distal extremities. Rare cases occur in the digestive tract and may be misdiagnosed with neuroendocrine or gastrointestinal stromal tumors. We aimed to specify the features of GT of the upper digestive tract.  We investigated two cases using whole exome sequencing (WES) and RNA-sequencing, and present clinical, histological, phenotypic and molecular features of 16 cases. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118896/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487177
Series		Accession: GSE118896	ID: 200118896

166. PRC2 activates interferon-stimulated genes indirectly by repressing miRNAs in glioblastoma
(Submitter supplied) Purpose: The goal of this study was to identify genes induced upon type I and II interferon response and how loss of PRC2/EZH2 impacts their induction. Methods: mRNA-seq from cells treated with universal type I IFN alpha/beta  or IFN gamma. miRNA-seq from GBM-derived tumor samples.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL16791 GPL18573 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133211/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA550390
Series		Accession: GSE133211	ID: 200133211

167. Transcriptional consequences of wild-type and missense mutant p53 in isogenic human acute myeloid leukemia (AML) cell lines
(Submitter supplied) TP53, encoding for the tumor suppressor p53, is the most frequently mutated gene in human cancer. The selective pressures shaping its mutational spectrum, dominated by missense mutations, have remained enigmatic, and neomorphic gain-of-function (GOF) activities have been implicated. We generated isogenic human leukemia cell lines of the most common TP53 missense mutations using CRISPR/Cas9. Functional, DNA binding, and transcriptional analyses revealed loss-of-function (LOF) without GOF effects of missense mutations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 96 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131592/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA544103
Series		Accession: GSE131592	ID: 200131592

168. Short and long-term effects of CDK4/6 inhibition on early stage breast cancer
(Submitter supplied) CDK4/6 inhibitors are used in the treatment of advanced estrogen receptor (ER)(+) breast cancer (BC). Their efficacy in ER(-) and early stage BC is currently under investigation. Here, we show that palbociclib, a CDK4/6 inhibitor, can inhibit both progression of ductal carcinoma in situ (DCIS) and growth of invasive disease in both an ER(-) basal BC model (MCFDCIS) and an ER(+) luminal model (MCF7 intraductal injection). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130903/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA541931
Series		Accession: GSE130903	ID: 200130903

169. H3K36me2 recruits DNMT3A and shapes intergenic DNA methylation landscapes
(Submitter supplied) Enzymes catalyzing CpG methylation in DNA, including DNMT1 and DNMT3A/B, are indispensable for mammalian tissue development and homeostasis. They are also implicated in human developmental disorders and cancers, supporting a critical role of DNA methylation during cell fate specification and maintenance. Recent studies suggest that histone post-translational modifications (PTMs) are involved in specifying patterns of DNMT localization and DNA methylation at promoters and actively transcribed gene bodies. more...
Organism:	Homo sapiens; Mus musculus; Drosophila melanogaster
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
8 related Platforms 43 Samples
FTP download: GEO (BW, TDF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118785/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486798
Series		Accession: GSE118785	ID: 200118785

170. Gene expression profile of OSSL_325096 treated myeloma cells
(Submitter supplied) OSSL_325096 is a compound that acts as p97/VCP inhibitor and induces apoptosis in myeloma cells. Therefore, we treated KMS12PE and KMS11 myeloma cell lines with OSSL_325096 or DMSO and compare gene expression levels to elucidate the mechanisms of apoptosis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118320/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485182
Series		Accession: GSE118320	ID: 200118320

171. Kallikrein-mediated cytokeratin 10 degradation is required for VZV propagation in skin
(Submitter supplied) Varicella Zoster Virus (VZV) is a skin-tropic virus that infects epidermal keratinocytes and causes chickenpox. Although common, VZV infection can be life-threatening particularly in the immunocompromised. Therefore, understanding VZV-keratinocyte interactions is important to find new treatments beyond vaccination and anti-viral drugs. In VZV- infected skin, Kallikrein 6 (KLK6), and the ubiquitin-ligase MDM2 are up-regulated concomitant with Keratin 10 (K10) down-regulation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21697 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136586/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA561812
Series		Accession: GSE136586	ID: 200136586

172. circNFIB suppresses lymphatic metastasis of pancreatic cancer
(Submitter supplied) Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignany and currently the fourth leading cause of cancer related death worldwide. Circular RNAs (circRNAs) are a kind of novel noncoding RNA with a covalently circular structure arise from the non-canonical splicing of precursor-mRNA(pre-mRNA). To identify circRNAs involved in the progression of PDAC, next-generation sequencing (NGS) was performed in five paired PDAC and normal adjacent tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL20795 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136569/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA562706
Series		Accession: GSE136569	ID: 200136569

173. Molecular basis of cisplatin resistance in testicular germ cell tumors
(Submitter supplied) The emergence of cisplatin (CDDP) resistance is the main cause of treatment failure and death in patients with testicular germ cell tumors (TGCT), but its biologic background is poorly understood. To study the molecular basis of CDDP resistance in TGCT we prepared and sequenced CDDP-exposed TGCT cell lines as well as 31 primary patients’ samples. Long-term exposure to CDDP increased the CDDP resistance 10 times in the NCCIT cell line, while no major resistance was achieved in Tera-2. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing
Platform: GPL18573 10 Samples
FTP download: GEO (CSV, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136560/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA562689
Series		Accession: GSE136560	ID: 200136560

174. Benchmarking NF-kB inhibitors
(Submitter supplied) We report the presence of the C11orf95-RELA fusion in cells isolated from a patient presenting with anaplastic ependymoma
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 1 Sample
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136559/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA562687
Series		Accession: GSE136559	ID: 200136559

175. RNA-seq analysis of control and ZC3H18-depleted ovarian cancer cells
(Submitter supplied) We report the differential gene expression in control versus ZC3H18-depleted OVCAR-8 cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136533/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA562626
Series		Accession: GSE136533	ID: 200136533

176. Gene expression changes associated with resistance to tagraxofusp (SL-401)
(Submitter supplied) The goal of this experiment was to determine the gene expression changes that occur in the setting of human leukemia cells with acquired resistance to tagraxofusp (SL-401), a recombinant interleukin 3 - diphtheria toxin fusion targeted cytotoxin
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131147/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA542719
Series		Accession: GSE131147	ID: 200131147

177. KSDM1b Role in Ewing Sarcoma
(Submitter supplied) This study looks at the  transcriptional profile of LSD2 knockdown in A673 Ewing sarcoma cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126275/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA521471
Series		Accession: GSE126275	ID: 200126275

178. Single-cell transcriptomic map of the human and mouse bladders
(Submitter supplied) A comprehensive cellular anatomy of normal human bladder is vital to address the cellular origins of benign bladder disease and bladder cancer. The physiological function and pathological changes of bladder are associated with its cell type. To investigate the classification and underlying function of bladder cells, we conducted single-cell RNA sequencing (scRNA seq) of 12,423 cells from human bladder and 12,884 cells from mouse bladder. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20795 GPL21273 5 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129845/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA532936
Series		Accession: GSE129845	ID: 200129845

179. Targets mediated microRNA arm-imbalance promotes gastric cancer progression
(Submitter supplied) Two miRNA arms from the same precursor, miR-574-5p and miR-574-3p, were reversely expressed and played exact opposite role in gastric cancer progression. miR-574-5p/-3p ratio was also strongly correlated with higher TNM stages and shorter survival of patients. The increase of miR-574-5p/-3p ratio, or the arm-imbalance of miR-574 was due to the dynamic expression of their highly complementary targets in gastric carcinogenesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112859/
Series		Accession: GSE112859	ID: 200112859

180. A novel fate-mapping approach allows intratumoral profiling of hypoxic cells II
(Submitter supplied) We designed a novel approach to fate-map hypoxic cells in order to determine their cellular response to physiological O2 gradients. Our system causes a change in the expressing fluorescent protein upon hypoxic exposure (DsRed -> GFP). We generated hypoxia fate-mapping tumors using MDA-MB-231 cells expressing our system. Metastatic lungs were resected 2 weeks after primary tumor removal, mechanically disrupted and digested with collagenase to obtain a cell suspension. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136372/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA562307
Series		Accession: GSE136372	ID: 200136372

181. Comparative gene expression in NCI-H716 cells grown in different glucose concentrations
(Submitter supplied) We performed RNA-Seq whole transcriptome analysis of H716 cells grown in two glucose concentrations.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136369/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA562299
Series		Accession: GSE136369	ID: 200136369

182. CTCF orchestrated enhancer hijacking accelerated tumorigenesis through remodeling 3D chromosomal architecture in NTS locus [RNA-seq]
(Submitter supplied) We identified aberrant CTCF binding lead to a 3D chromosomal interactional driver in NTS locus that accelerates tumorigenesis of uveal melanoma. Both enhancer deletion and abolishing CTCF binding lead to the loss of chromosomal looping and triggered therapeutic efficacy in inhibiting tumorigenesis. Our study shed light on a functional chromosomal architecture induced enhancer hijacking, thereby provide novel concept of 3D-chromosomal conformation exploration.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136338/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA562258
Series		Accession: GSE136338	ID: 200136338

183. Enterovirus 71 oncolysis of malignant gliomas
(Submitter supplied) This study finds that EV71 has oncolytic activity against experimental human malignant gliomas. RNA-seq analysis of infected glioma cells reveals transcriptional up-regulation, notably genes in apoptosis pathways. Application of virus targeting based on brain-specific microRNA-124 enhances the safety profile. Oncolysis with EV71 may be a potentially novel treatment for malignant gliomas.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136330/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA562271
Series		Accession: GSE136330	ID: 200136330

184. Selective Disruption of Core Regulatory Transcription [single cell RNA-seq]
(Submitter supplied) Activation of identity determining transcription factors (TFs), or core regulatory TFs, is governed by cell-type specific enhancers, an important subset of these being super enhancers (SEs). This mechanism is distinct from constitutive expression of housekeeping genes. The characterization of drug-like small molecules to selectively inhibit core regulatory circuitry is of high interest for treatment of cancers, which are addicted to core regulatory TF function at SEs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121107/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA495670
Series		Accession: GSE121107	ID: 200121107

185. Profiling of EMT-associated mitochondrial RNAs in hepatocellular carcinoma cells
(Submitter supplied) Mitochondria, the powerhouse of the cell, has been recognized as the key players in cancer cell biology, including cancer metabolism, metastasis, and drug resistance. Recent studies have demonstrated a functional interplay between mitochondria and epithelial-mesenchymal transition (EMT) in cancer. To delineate the role of mitochondrial components in this interplay, we induced the EMT in hepatoma HepG2 cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119946/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490756
Series		Accession: GSE119946	ID: 200119946

186. In vivo epigenetic editing of Sema6a promoter reverses impaired transcallosal connectivity caused by C11orf46/ARL14EP neurodevelopmental risk gene
(Submitter supplied) Many neuropsychiatric risk genes contribute to epigenetic regulation of gene expression but very little is known about specific chromatin-associated mechanisms governing the formation and maintenance of neuronal connectivity. Here we show that transcallosal connectivity is critically dependent on C11orf46 (also known as ARL14EP), a small nuclear protein encoded in the chromosome 11p13 Wilms Tumor, Aniridia, Genitourinary Abnormalities, intellectual disability (formerly referred to as Mental Retardation) (WAGR) risk locus. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119360/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488832
Series		Accession: GSE119360	ID: 200119360

187. Glioblastoma multiforme cancer stem cells from different patients exhibit consistent gene expression and mechanical phenotypes across distinct states in culture
(Submitter supplied) Cancer stem cells are responsible for the regenerative properties of tumors, manifested as recurrence and metastasis. They can adopt different states, some of which may not be sensitive to current therapies. Modeling distinct states in culture will contribute towards efficient drug discovery. We previously demonstrated that putative cancer stem cells from multiple glioblastoma patients can be efficiently maintained under different signal transduction states by means of different culture conditions; each state is marked by different levels of STAT3 phosphorylation and Hes3 expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 27 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77751/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA311347
Series		Accession: GSE77751	ID: 200077751

188. Deep sequencing of GSK-126 treated HER2+ PDX tumours
(Submitter supplied) Monoclonal antibodies (mAbs) targeting the oncogenic receptor tyrosine kinase ERBB2/HER2, such as Trastuzumab, are the standard of care therapy for breast cancers driven by ERBB2 overexpression and activation. However, a substantial proportion of patients exhibits de novo resistance. Here, by comparing matched Trastuzumab-naïve and post-treatment patient samples from a neoadjuvant trial, we link resistance with elevation of H3K27me3, a repressive histone modification catalyzed by Polycomb Repressor Complex 2 (PRC2). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136300/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA562076
Series		Accession: GSE136300	ID: 200136300

189. Hsa-miR-139-5p/HNRNPF axis modulates gene-transcripts balance in thyroid cancer cells
(Submitter supplied) We explored alternative splicing events upon hsa-miR-139-5p/HNRNPF axis regulation in our cell system using the Multivariate Analysis of Transcript Splicing (rMATS) computational tool (https://doi.org/10.1073/pnas.1419161111). Differential analysis of major splicing outcomes (skipped exon, alternative 5’/3’ splice, mutually exclusive exons and retained intron) revealed a total of 174 events significantly activated or repressed (FDR<0.05) upon HNRNPF regulation.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123680/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509567
Series		Accession: GSE123680	ID: 200123680

190. mRNA gene expression profiling in a human AML cell line treated with small molecule inhibitors that impact different RNA polymerase transcription complexes, or their combination, in comparison to a global DNA-damaging anthracycline compound
(Submitter supplied) Our results confirmed that CX-5461, a Pol I inhibitor, does not significantly impact mRNA expression at 6 hrs, while I-BET151 alone, known to inhibit MYC and expression of other oncognes, resulted in widespread changes in select gene expression programs as previously demonstrated (Dawson et al., 2011). Interestingly, the combination of CX-5461 and I-BET151 demonstrated no further gene expression changes from I-BET151 alone, suggesting that their mechanism of synergy is more likely directly associated with the CX-5461-mediated DNA damage response. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118565/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486093
Series		Accession: GSE118565	ID: 200118565

191. N-Myc-mediated epigenetic reprogramming drives lineage plasticity in advanced prostate cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL16791 GPL21103 92 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117306/
Series		Accession: GSE117306	ID: 200117306

192. N-Myc-mediated epigenetic reprogramming drives lineage plasticity in advanced prostate cancer [RNA-seq]
(Submitter supplied) Despite recent advances in highly effective androgen receptor (AR)-directed therapies for the treatment of prostate cancer, a significant subset of patients with resistant disease develop AR-null, androgen signaling-indifferent neuroendocrine prostate cancer (NEPC). A majority of these NEPC cases that arise following anti-androgen therapy are driven by the aberrant expression of the transcription factor N-Myc. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL21103 38 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117305/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481738
Series		Accession: GSE117305	ID: 200117305

193. TFPa/HADHA is required for fatty acid beta-oxidation and cardiolipin re-modeling in human cardiomyocytes
(Submitter supplied) Mitochondrial trifunctional protein deficiency, due to mutations in hydratase subunit A (HADHA), results in sudden infant death syndrome with no cure.  To reveal the disease etiology, we generated stem cell-derived cardiomyocytes from HADHA-deficient hiPSCs and accelerated their maturation via an engineered microRNA maturation cocktail that upregulated the epigenetic regulator, HOPX.  Here we report, matured HADHA mutant cardiomyocytes treated with an endogenous mixture of fatty acids manifest the disease phenotype: defective calcium dynamics and repolarization kinetics which results in a pro-arrhythmic state. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL23227 28 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135595/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA559385
Series		Accession: GSE135595	ID: 200135595

194. Targets mediated microRNA arm-imbalance promotes gastric cancer progression [lncRNA]
(Submitter supplied) Two miRNA arms from the same precursor, miR-574-5p and miR-574-3p, were reversely expressed and played exact opposite role in gastric cancer progression. miR-574-5p/-3p ratio was also strongly correlated with higher TNM stages and shorter survival of patients. The increase of miR-574-5p/-3p ratio, or the arm-imbalance of miR-574 was due to the dynamic expression of their highly complementary targets in gastric carcinogenesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133629/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA552063
Series		Accession: GSE133629	ID: 200133629

195. Phosphoethanolamine Accumulation Protects Cancer Cells under Glutamine Starvation through Downregulation of PCYT2
(Submitter supplied) The conditions of the tumor microenvironment, such as nutrient starvation, play critical roles in cancer progression. However, the role of glutamine deprivation in cancer progression is not studied as extensively as that of hypoxia. Here, we show that glutamine starvation triggered down-regulation of PCYT2 by stimulating accumulation of PEtn. Interestingly, glutamine upregulated series of glutamine-responsive genes, not only PCYT2. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136289/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA561847
Series		Accession: GSE136289	ID: 200136289

196. Genome wide transcriptome analysis of palbociclib or GSK3326595 treated A375 cells [Palbociclib_GSK_RNASeq]
(Submitter supplied) RNA-seq was performed to  compare the transcriptional programmes of A375 cells treated with Palbociclib or GSK3326595 compared to untreated cells Cyclin dependent kinase 4/6 (CDK4/6) inhibitors are an established treatment in estrogen receptor positive breast cancer and are currently in clinical development in melanoma; a tumour that exhibits high rates of CDK4 activation. We analyzed melanoma cells with acquired resistance to the CDK4/6 inhibitor palbociclib, and demonstrated that palbociclib-mediated inhibition of PRMT5 is essential for sensitivity to CDK4/6 inhibitors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133568/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA551945
Series		Accession: GSE133568	ID: 200133568

197. Gene expression alterations associated with acquired-resistance to the CDK4/6 inhibitor palbociclib [Palbociclib resistance_RNASeq]
(Submitter supplied) RNA-seq was performed to  compare the transcriptional programmes of palbociclib-resistant A375 and CHL1 cells compared to their parental counterparts Cyclin dependent kinase 4/6 (CDK4/6) inhibitors are an established treatment in estrogen receptor positive breast cancer and are currently in clinical development in melanoma; a tumour that exhibits high rates of CDK4 activation. We analyzed melanoma cells with acquired resistance to the CDK4/6 inhibitor palbociclib, and demonstrated that palbociclib-mediated inhibition of PRMT5 is essential for sensitivity to CDK4/6 inhibitors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133567/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA551944
Series		Accession: GSE133567	ID: 200133567

198. A Novel PI3K Regulator, ARID4B, Presents Synthetic Essentiality in PTEN-deficient Prostate Cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 8 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116670/
Series		Accession: GSE116670	ID: 200116670

199. A Novel PI3K Regulator, ARID4B, Presents Synthetic Essentiality in PTEN-deficient Prostate Cancer [RNA-seq]
(Submitter supplied) Phosphatase and tensin homologue (PTEN) is the most frequently mutated tumor suppressor gene in human prostate cancer. Synthetic essentiality is defined as cancer that harbors a specific tumor suppressor deficiency is dependent on synthetic-essential genes for the malignant phenotypes. Recently, targeting such synthetic-essential genes has become an attractive treatment approach for cancers that acquire loss-of-function mutations in tumor suppressor genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116668/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA479842
Series		Accession: GSE116668	ID: 200116668

200. Deconvolution of melanoma transcriptomes and miRNomes by independent component analysis
(Submitter supplied) The repositories for various “omics” data collected from different cancer types are constantly growing. However, robust diagnostic and/or prognostic conclusions can often not be extracted from mixed transcriptomes or other heterogenous datasets obtained from large cohorts as important signals or single features can be masked. Here, computational microdissection of bulk transcriptome data was applied to gain insights into patient prognosis and to investigate important processes and cell subtypes within new samples in silico. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116111/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA477296
Series		Accession: GSE116111	ID: 200116111

201. Gene expression profiling in lung and breast cancer cells treated by Bloom-specific siRNAs
(Submitter supplied) A549 and MDA-MB-231 cells were transfected with the Bloom-specific siRNA. Total RNA was extracted using Trizol at 48 hours after transfection. RNA-SEQ was carried out to profile the gene expression in both culture conditions.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136105/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA561309
Series		Accession: GSE136105	ID: 200136105

202. Regulation of PRMT5-MDM4 axis is critical in the response to CDK4/6 inhibitors in melanoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL18573 18 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133670/
Series		Accession: GSE133670	ID: 200133670

203. Epigenetic reprogramming of immune cells in women with PCOS impact genes controlling reproductive function
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18573 41 Samples
FTP download: GEO (COV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130582/
Series		Accession: GSE130582	ID: 200130582

204. Epigenetic reprogramming of immune cells in women with PCOS impact genes controlling reproductive function [RNAseq]
(Submitter supplied) Transcriptomic and genome-wide DNA methylation was performed on T helper cells using RNA-sequencing and Reduced Representation Bisulfite Sequencing, respectively. Specific genome-wide DNA methylation analysis of T helper cells from women with PCOS identified 5,581 differentially methylated CpG sites. Interestingly, functional gene ontology enrichment analysis showed that genes located at the proximity of differentially methylated CpG sites belong to pathways related to reproductive function and immune cell function. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 11 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130580/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540679
Series		Accession: GSE130580	ID: 200130580

205. The EN1 transcription factor drives neural features and brain metastases in triple negative breats cancer (TNBC)
(Submitter supplied) To define transcriptional dependencies of TNBCs, we identified transcription factors highly and specifically expressed in primary TNBCs and tested their requirement for cell growth in a panel of breast cancer cell lines. We found that EN1 is overexpressed in TNBCs and its downregulation preferentially and significantly reduces cellular viability and tumorigenicity in TNBC cell lines. Based on RNA-seq and ChIPseq we found that EN1 regulates genes involved in angiogenesis, neurogenesis, and axon guidance in breast cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 89 Samples
FTP download: GEO (BED, CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120957/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA495138
Series		Accession: GSE120957	ID: 200120957

206. Genome-wide RNA-seq from GALNT14-depleted and GALNT14 overexpressing MDA-MB-231 LM2 and Par cells
(Submitter supplied) Purpose: To identify downstream signaling pathways that mediate functions of GALNT14 Methods: RNAs isolated from MDA231-LM2 cells expressing shCntr or shGALNT14 and MDA231-Par cells expressing pBabe-Hygro control vector or GALNT14 expression vector were analyzed by using an Illumina HiSeq 2500 Conclusions: Our study represents the first transcriptome profile of GALNT14-depleted MDA231-LM2 and GALNT14-overexpressing Par cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (BW, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72111/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA293035
Series		Accession: GSE72111	ID: 200072111

207. Chronic cadmium exposure decreases the dependency of MCF7 breast cancer cells on ERα
(Submitter supplied) To understand how chronic cadmium exposure alters the dependency of ERα in terms of gene expression, we transiently silenced ERα using ICI, an antiestrogen that promotes the degradation of ERα. MCF7 and cadmium-adapted cells (Cd7 and Cd12) were treated with ICI to mediate the degradation of ERα, and a nonbiased global gene expression analysis was conducted using RNA-seq.  MCF7 shared 67.3% and 59.5% of the DE genes with Cd7 and Cd12 cells, respectively, suggesting that ERα continues to play an important role in regulating the expression of genes following chronic cadmium exposure. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134127/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA554005
Series		Accession: GSE134127	ID: 200134127

208. Enhanced hemato-endothelial specification during human embryonic development through developmental cooperation between AF4-MLL and MLL-AF4 fusions
(Submitter supplied) The t(4;11)(q21;q23) translocation is associated with high-risk infant pro-B-cell acute lymphoblastic leukemia (B-ALL) and arises prenatally during embryonic/fetal hematopoiesis. The developmental/pathogenic contribution of the t(4;11)-resulting MLL-AF4 (MA4) and AF4-MLL (A4M) fusions remains enigmatic; MA4 is always expressed in t(4;11)+B-ALL patients, but the reciprocal fusion A4M is expressed in only 50% of patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118947/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487464
Series		Accession: GSE118947	ID: 200118947

209. Cyclophosphamide (CTX) Enhances Cancer Antibody Immunotherapy in the Resistant Bone Marrow Niche by Modulating Macrophage FcγR Expression
(Submitter supplied) Purpose: To understand the molecular mechanisms underlying the CTX synergization with antibody therapies in resistant niche-specific organs and BM-resident tumors
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135997/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA560906
Series		Accession: GSE135997	ID: 200135997

210. CDK12 inhibition in Hep3B, Huh7 and SNU449 cells
(Submitter supplied) Purpose: to analyze gene expression in THZ531 treated liver cancer cells. Methods: Hep3B and Huh7 cells are treated with THZ531 for 24 hours. SNU449 cells are treated with THZ531 for 48 hours. For RNA sequencing, the library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina). Gene set enrichment analysis was performed using gene set enrichment analysis software.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135960/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA560783
Series		Accession: GSE135960	ID: 200135960

211. A new strategy for identifying mechanisms of drug-drug interaction using transcriptome analysis: Compound Kushen injection as a proof of principle
(Submitter supplied) Drug-drug interactions (DDIs), especially with herbal medicines, are complex, making it difficult to identify potential molecular mechanisms and targets. We introduce a workflow to carry out DDI research using transcriptome analysis and interactions of a complex herbal mixture, Compound Kushen Injection (CKI), with cancer chemotherapy drugs, as a proof of principle. Using CKI combined with doxorubicin or 5-Fu on cancer cells as a model, we found that CKI enhanced the cytotoxic effects of doxorubicin on A431 cells while protecting MDA-MB-231 cells treated with 5-Fu. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 27 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130359/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA539875
Series		Accession: GSE130359	ID: 200130359

212. Understanding the Mechanistic Contribution of Herbal Extracts in Compound Kushen Injection with Transcriptome Analysis
(Submitter supplied) Herbal compatibility is the knowledge of which herbs to combine in traditional Chinese medicine (TCM) formulations. The lack of understanding of herbal compatibility is one of the key problems for the application and popularization of TCM in western society. Because of the chemical complexity of herbal medicines, it is simpler to begin to conduct compatibility research based on herbs rather than component plant secondary metabolites. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 9 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130358/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA539874
Series		Accession: GSE130358	ID: 200130358

213. PRMT5 methylome profiling uncovers a direct link to splicing regulation in human acute myeloid leukemia
(Submitter supplied) Protein arginine methyltransferase 5 (PRMT5) belongs to the class II arginine methyltransferases and catalyzes monomethylation and symmetrical dimethylation of arginines on proteins. It has recently emerged as a promising cancer drug target, and three PRMT5 inhibitors are currently in clinical trials for a range of malignancies. In this study, we aimed to further elucidate the role of PRMT5 in acute myeloid leukemia (AML). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL18573 4 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129652/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA532395
Series		Accession: GSE129652	ID: 200129652

214. β-catenin/Tcf7l2 dependent transcriptional regulation of GLUT1 gene expression by Zic family proteins in colon cancer
(Submitter supplied) The Zinc finger of the cerebellum (ZIC) proteins have been implicated to function in normal tissue development. Mutations or deletions of ZIC genes have been found to be associated with neural-related abnormalities. Recent studies point out the critical functions of Zic proteins in cancers and the potential tumor suppressive functions in colon cancer development and progression. To elucidate the functional roles of Zic proteins in colorectal cancer, we employed CRISPR/Cas9 genome editing to knock out the Zic5 gene and analyze the chromatin localization pattern and transcriptional regulation of target gene expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 51 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127960/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA525873
Series		Accession: GSE127960	ID: 200127960

215. CDK7 inhibition suppresses Castration-Resistant Prostate Cancer through MED1 inactivation
(Submitter supplied) We performed RNA-seq and ChIP-seq in three prostate cell lines (VCaP, LNCaP and DU145) to ascertain the role of the mediator complex MED1 in AR signaling. Upon androgen stimulation, MED1 undergoes phosphorylation by CDK7 and physically engages with AR at super-enhancer sites, which is essential for AR-mediated transcription. The CDK7 specific inhibitor THZ1 blunts AR-dependent neoplastic growth by preventing the co-recruitment of AR/MED1 in a genome-wide fashion, and reverts the enzalutamide resistance characterized by hyper-phosphorylated MED1. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 53 Samples
FTP download: GEO (BW, CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125245/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515688
Series		Accession: GSE125245	ID: 200125245

216. Organoid-induced differentiation of conventional T cells from human pluripotent stem cells
(Submitter supplied) Generation of T cells from pluripotent stem cells (PSC) has the potential to transform adoptive immunotherapy for cancer into universal donor, off-the-shelf cellular therapies.  However, differentiation of human PSCs into fully mature T cells has been challenging with existing methods. We report that a 3D organoid method permitted efficient differentiation of human embryonic stem cell and induced pluripotent stem cell-derived mesoderm progenitors to mature, functional conventional T cells with a diverse T cell receptor (TCR) repertoire. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 32 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116015/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476793
Series		Accession: GSE116015	ID: 200116015

217. Myoepithelial cell perturbations in BRCA mutation carriers and in DCIS (ductal carcinoma in situ)
(Submitter supplied) We describe the gene expression profiles and enhancer landscape of normal myoepithelial cells and perturbations of these in BRCA1 and BRCA2 mutation carriers and in DCIS. We identified a myoepithelial transcription regulatory network orchestrated by p63 and TCF7 and defined the genomic targets of these transcription factors by ChIP-seq. While the majority of myoepithelial cells co-express p63 and TCF7 in normal breast of healthy women, the frequency of these cells is significantly lower in BRCA1 mutation carriers and in DCIS. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL9052 54 Samples
FTP download: GEO (BED, NARROWPEAK, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113909/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454454
Series		Accession: GSE113909	ID: 200113909

218. BS008, an amiloride derivative, can regulate the alternative splicing of multiple gene transcripts in cancer cells
(Submitter supplied) Alternative splicing (AS) is a process that enables a mRNA to generate different protein isoforms that may have different biological functions or properties. Cancer cells often use this maneuverability to produce proteins that contribute to growth and survival. In previous study, we found that the antihypertensive drug amiloride has a novel biological function that regulates the AS on human cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110059/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432711
Series		Accession: GSE110059	ID: 200110059

219. Transcriptome analysis in Neobractatin treated cells
(Submitter supplied) The goal of this study is to use RNA seq and rMATS analysis to identify the anticancer mechanism of novel compounds
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108706/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA428359
Series		Accession: GSE108706	ID: 200108706

220. Glioma Stem Cell Specific Super Enhancer Drives Polyunsaturated Fatty Acid Synthesis to Support EGFR Signaling
(Submitter supplied) Glioblastoma ranks among the most aggressive and lethal of all human cancers. Functionally defined glioma stem cells (GSCs) contribute to this poor prognosis by driving therapeutic resistance and maintenance of cellular heterogeneity. To understand the molecular processes essential for GSC maintenance and tumorigenicity, we interrogated the super-enhancer landscapes of primary glioblastoma specimens and in vitro GSCs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130648/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540966
Series		Accession: GSE130648	ID: 200130648

221. Analysis of transcriptome changes following SOX2 knockdown in three different Ewing sarcoma cell lines
(Submitter supplied) We report that knockdown of SOX2 in Ewing sarcoma cell lines promotes changes in the expression of several genes that are involved a variety of molecular processes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124221/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA511006
Series		Accession: GSE124221	ID: 200124221

222. RNA-Seq study of Cell lines rendered resistant to idelalisib and ibrutinib
(Submitter supplied) BCR pathway inhibitors idelalisib and ibrutinib are the first small molecule targeted agents for B-cell malignancies. In spite of encouraging response rates in various forms of B cell diseases, patients will eventually develop relapse due to the emergence of resistant cells. To better identify the possible mechanisms of resistance we developed and characterized idelalisib- and ibrutinib-resistant variants of the human non Hodgkin’s lymphoma cell lines DoHH2 and Daudi. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118707/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486519
Series		Accession: GSE118707	ID: 200118707

223. Sirt6 Oncogene Mediates PI3K/Akt Signaling Activation in Diffuse Large B-Cell Lymphoma
(Submitter supplied) Purpose:Sirtuin 6 (Sirt6) is a highly conserved ADP-ribosylase and NAD+ dependent deacylase, involved in broad cellular processes. This molecule possesses contradictory roles in carcinogenesis, as it has been documented to both suppress and augment tumor growth. This experiment aimed to document the Sirt6 expression and functions in diffuse large B-cell lymphoma (DLBCL). Methods:Immunohistochemistry was conducted to assess the expression of Sirt6 on paraffin-embedded tissues from 70 DLBCL patients and 35 reactive hyperplasia patients with informed contents. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135914/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA560560
Series		Accession: GSE135914	ID: 200135914

224. Single nucleotide polymorphism rs13426236 contributes to an increased prostate cancer risk via regulating MLPH splicing variant 4
(Submitter supplied) A prostate cancer risk single nucleotide polymorphism (SNP), rs13426236, is significantly associated with melanophilin (MLPH) expression. To functionally characterize role of the rs13426236 in prostate cancer, we first performed splicing-specific expression Quantitative Trait Loci (eQTL) analysis and refined the significant association of rs13426236 allele G with an increased expression of MLPH splicing variant 4 (V4) (P= 7.61E-5) but not other protein-coding variants (V1-V3) (P>0.05). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135888/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA560419
Series		Accession: GSE135888	ID: 200135888

225. Transcriptomic analyssis following EHMT1/2 inhibition
(Submitter supplied) RNA was isolated from PEO1 olaparib resistant (PEO1-OR) cells grown in complete growth media or PEO1-OR clone 4 cells grown in complete growth media with 500 nanomolar of UNC0642 for 72 hrs. RNA-sequencing was performed to evaluate UNC0642-dependent transcriptional reprogramming, which contributes to resensitization of PEO1-OR to olaparib. PEO1 line was authenticated prior to sequencing. PEO1 parental were confirmed to be BRCA2-mutated (5139C>G).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135864/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA560367
Series		Accession: GSE135864	ID: 200135864

226. Cooperation of dominant oncogenes with regulatory variants shapes clinical outcomes in pediatric cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 20 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119972/
Series		Accession: GSE119972	ID: 200119972

227. RNA-seq of three Ewing sarcoma cell lines (A673, SK-N-MC, RDES), transfected with either siControl or siMYBL2.
(Submitter supplied) Deciphering principles of inter-individual tumor heterogeneity is essential for refinement of personalized anti-cancer therapy. Unlike cancers of adulthood, pediatric malignancies including Ewing sarcoma feature a striking paucity of somatic alterations except for pathognomonic driver-mutations that cannot explain overt variations in clinical outcome. Here we demonstrate in the Ewing sarcoma model how cooperation of a dominant oncogene and regulatory variants determine tumor growth, patient survival and drug response. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119970/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490875
Series		Accession: GSE119970	ID: 200119970

228. Extracellular RNA in a single droplet of human serum reflects physiologic and disease states
(Submitter supplied) We developed SILVER-seq (Small Input Liquid Volume Extracellular RNA Sequencing) to efficiently sequence both integral and fragmented cfRNAs from a small droplet (5-7 microliters) of liquid biopsy. We carried out SILVER-seq on more than 150 serum droplets from male and female donors ranging from 19 to 48 years of age. SILVER-seq detected cfRNAs from more than a quarter of the human genes, including small RNAs and fragments of mRNAs and long non-coding RNAs (lincRNAs).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 128 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131512/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA543872
Series		Accession: GSE131512	ID: 200131512

229. Tumor intrinsic PRMT5 inhibition through MTAP loss predicts response to the first-in-class type I PRMT inhibitor, GSK3368715
(Submitter supplied) Type I Protein Arginine Methyltransferases (PRMTs) catalyze asymmetric dimethylation of arginine (ADMA) residues on numerous protein substrates to modulate their activity. Type I PRMTs and many of their substrates have been implicated in human cancers, suggesting that inhibiting Type I PRMT activity offers a tractable approach for therapeutic intervention. The current report describes GSK3368715 (EPZ019997), a potent, reversible Type I PRMT inhibitor with anti-tumor activity against human cancer cells both in vitro and in vivo. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 32 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126651/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA522801
Series		Accession: GSE126651	ID: 200126651

230. Next generation sequencing quantitatively analyzes transcriptomes of primary CLL cells co-culture with Wild Type or prkcb-/- bone marrow mesenchymal stromal cells
(Submitter supplied) RNA-seq profiles of patient-derived primary CLL cells when co-cultured with bone marrow derived mesenchymal stromal cells (BMSC) from either wildtype or Prkcb-/- mice, in normal condition or under venetoclax (ABT-199) treatment.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119808/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490359
Series		Accession: GSE119808	ID: 200119808

231. BCL6 confers KRAS-mutant NSCLCs resistance to BET inhibitors
(Submitter supplied) We report that OTX015 upregulates BCL6 in KRAS-mutant NSCLC cells. Considering that both BCL6 and BET proteins regulate target genes by affecting transcription, we performed an RNA-seq experiment to identify downstream genes which response to OTX015. Retinal mRNA profiles of A549 cells treated with DMSO (0.1% for 6 hr) and OTX015 (1 μM for 6 hr) were generated by deep sequencing, in triplicate, using the SOLiD v4 sequencing platform. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118645/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486332
Series		Accession: GSE118645	ID: 200118645

232. Growth Differentiation Factor 11 exacerbates non-alcoholic fatty liver disease in vitro and in vivo
(Submitter supplied) Growth differentiation factor 11 (GDF11), also known as bone morphogenetic protein 11 (BMP11) is a member of the Growth differentiation factors (GDFs), a subfamily of proteins belonging to the transforming growth factor-beta (TGF-β) superfamily (Katoh and Katoh 2006).  ). In the past 7-8 years, several high profile studies, showed that systemic restoration of GDF11 levels reverses age-related phenotypes and rejuvenated heart and skeletal muscle in aged mice (Loffredo, Steinhauser et al. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135796/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA560078
Series		Accession: GSE135796	ID: 200135796

233. Gene expression profiles of tumor-infiltrating CD8 T cells in hepatocellular carcinoma
(Submitter supplied) We report the gene expression profiles of MACS-sorted tumor-infiltrating CD8 T cells in hepatocellular carcinoma.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132812/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA549153
Series		Accession: GSE132812	ID: 200132812

234. Gene expression profiles of 4-1BB+PD-1-high, 4-1BB-PD-1-high, and PD-1-int tumor-infiltrating CD8 T cells in hepatocellular carcinoma
(Submitter supplied) We report the gene expression profiles of FACS-sorted 4-1BB+PD-1-high, 4-1BB-PD-1-high, and PD-1-int tumor-infiltrating CD8 T cells in hepatocellular carcinoma.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132810/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA549151
Series		Accession: GSE132810	ID: 200132810

235. NAPRT activation of macrophages
(Submitter supplied) Damage-associated molecular patterns (DAMPs) are molecules that can be actively or passively released by injured tissues and that activate the immune system. Here we show for the first time that the NAD biosynthetic enzyme nicotinate phosphoribosyltransferase (NAPRT), the rate-limiting enzymes in the intracellular synthesis of NAD from nicotinic acid, is physiologically present in human sera, where it acts as a novel DAMP. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135753/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA559895
Series		Accession: GSE135753	ID: 200135753

236. Loss of 9p21 regulatory hub promotes kidney cancer progression by upregulating HOXB13
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 15 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135719/
Series		Accession: GSE135719	ID: 200135719

237. Absence of NKG2D ligands defines human leukaemia stem cells and mediates their immune evasion
(Submitter supplied) Patients with acute myeloid leukaemia (AML) often achieve remission yet subsequently die of disease relapse, which is commonly driven by chemotherapy-resistant  leukaemic stem cells (LSCs). LSCs are defined by their capacity to initiate leukaemia in immuno-compromised mice. This precludes an analysis of their interaction with lymphocytes as components of anti-tumour immunity, which LSCs must escape in order to induce cancer7. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127959/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA525870
Series		Accession: GSE127959	ID: 200127959

238. Therapeutic targeting of RNA splicing catalysis through inhibition of protein arginine methylation
(Submitter supplied) RNAseq of samples to identify changes in gene expression upon SRSF2 mutation
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL19057 GPL20301 48 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123774/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509783
Series		Accession: GSE123774	ID: 200123774

239. Total RNA-seq in patients with hematological malignancy
(Submitter supplied) Immune response and leukocyte activation genes are upregulated following 5-azacitidine treatment
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL18573 63 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118558/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486089
Series		Accession: GSE118558	ID: 200118558

240. N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis 
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other; Methylation profiling by high throughput sequencing
Platform: GPL11154 62 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106124/
Series		Accession: GSE106124	ID: 200106124

241. Pleiotropic impact of DNA-PK in cancer and implications to therapeutic strategies
(Submitter supplied) DNA-dependent protein kinase catalitic subunit (DNA-PK) is associated with aggressive disease. DNA-PK plays a role in transcriptional regulation of cancer-relevent pathways but it is not well understood.  This study uses transcriptomic analyses to understand the transcriptional role of DNA-PK in castration resistent prostate cancer (CRPC) upon DNA-PK inhibition
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 29 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116765/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480169
Series		Accession: GSE116765	ID: 200116765

242. SMUG1 promotes telomere maintenance through telomerase RNA end-processing
(Submitter supplied) Single-strand selective uracil DNA-glycosylase (SMUG1) associates with the DKC1-H/ACA ribonucleoprotein complex, which is essential for telomerase biogenesis. We show herein, that SMUG1 interacts with the telomerase RNA component, hTERC, and is required for co-transcriptional processing of the nascent transcript towards mature hTERC. We demonstrate that SMUG1 regulates the presence of base modifications between the CR4/CR5 region and the H-box situated towards the 3´-end of hTERC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL15520 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116580/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA479447
Series		Accession: GSE116580	ID: 200116580

243. Robust hepatitis E virus infection and transcriptional response in human hepatocytes
(Submitter supplied) In this study, we established a protocol based on the HEV genotype 3 p6 (Kernow C-1) and the human hepatoma cell lines HepG2 and HepG2/C3A with different media conditions to produce HEV cell culture-derived particles (HEVcc) with viral titers between 10e5 to 10e6 FFU/mL. Viral titers could be further enhanced by an HEV variant harboring a mutation in the RNA-dependent RNA polymerase. These HEVcc particles were infectious in primary human hepatocytes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 24 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135619/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA559467
Series		Accession: GSE135619	ID: 200135619

244. Regulation of TERT and HKR3 in Hep3B cell lines
(Submitter supplied) The TERT and HKR3 mechanism regulating cell cycle related expression changes remains unknown during HCC progress. We evaluated the relationship between hTERT expression and human kruppel-related 3 (HKR3) and cell cycle-related factors in Hep3B cell lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135581/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA559360
Series		Accession: GSE135581	ID: 200135581

245. Next Generation Sequencing Facilitates Quantitative Analysis of HePG2i cell line with and without DOX induced GATA4 expression Transcriptomes
(Submitter supplied) HePG2i cell line mRNA profiles of DOX induced GATA4 expression and non-DOX induced were generated by deep sequencing, in triplicate, using Illumina HiSeq 10000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 2 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135579/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA559361
Series		Accession: GSE135579	ID: 200135579

246. Epigenetic Pathways of HDAC Inhibitor Resistance in Cutaneous T Cell Lymphoma
(Submitter supplied) Epigenetic changes deregulate gene expression to drive oncogenesis. The reversible nature of these changes enables therapeutic targeting, as in cutaneous T-cell lymphoma (MF/SS), Histone deacetylase inhibitors (HDACi), which alter epigenetic modifications, are effective in ~30% of MF/SS patients. However, there are no markers that predict MF/SS progression or therapy resistance. We hypothesized that epigenetic alterations drive MF/SS progression and promote HDACi drug resistance. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL21290 88 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132053/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA545731
Series		Accession: GSE132053	ID: 200132053

247. Tumors with TSC mutations are sensitive to CDK7 inhibition through NRF2 and glutathione depletion
(Submitter supplied) We report the global gene expression effects in TSC-deficient and TSC wild type cells after treatemnet with. CDK7 inhibitor(THZ1), we performed RNA-Seq on TSC1-null HCV.29 cells and TSC1-intact HCV.29 cells treated with 30nM THZ1, and with 100nM THZ1, for 6 hours. Many genes showed marked changes in expression in comparison with control untreated cells.  Furthermore, 1128 genes showed > 5-fold lower expression in 30nM THZ1-treated TSC1-null HCV.29 cells compared with 30nM THZ1-treated TSC1-intact HCV.29 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135527/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA559171
Series		Accession: GSE135527	ID: 200135527

248. Tumor Heterogeneity in Metastatic Potential is Indicated by Adhesion Strength
(Submitter supplied) Tumors are heterogeneous and comprised of cells with varying function and ability to disseminate. Despite significant effort, no universal biological marker currently serves as a metric for metastatic potential of solid tumors. Common to disseminating cells from such tumors, however, is the need to modulate their adhesion as they detach from the tumor and migrate through stroma to intravasate. Adhesion strength is heterogeneous even amongst cancer cells within a given population, and using a parallel plate flow chamber, we separated and sorted these populations into weakly and strongly adherent groups; when cultured under stromal conditions, this adhesion phenotype is stable over multiple days, sorting cycles, and common across all epithelial tumor lines investigated. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135515/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA559156
Series		Accession: GSE135515	ID: 200135515

249. PT2385 HIF2A inhibitor treatment of patient derived orthotopic xenograft neuroblastoma cells in the presence or absence of hypoxia
(Submitter supplied) neuroblastoma cells derived from PDOX models were treated with the HIF2A inhibitor in normoxic and hypoxic conditions.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135487/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA559082
Series		Accession: GSE135487	ID: 200135487

250. Transcriptomic profiles of Pcy and Pdk2KO mice and human kidney epithelial cells treated with RGLS4326
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL19057 71 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134721/
Series		Accession: GSE134721	ID: 200134721

251. Transcriptomic profile of human kidney epithelial cells - derived from cysts of ADPKD donors
(Submitter supplied) We utilized primary cyst cultures derived from human ADPKD donors transfected with RGLS4326 to demonstrate the human translational potential of RGLS4326.  Results show that RGLS4326 treatment globally de-repressed mRNAs of predicted miR-17 target genes in primary human ADPDK cyst cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134720/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA556225
Series		Accession: GSE134720	ID: 200134720

252. Exploring genetic interaction manifolds constructed from rich phenotypes
(Submitter supplied) Rich phenotyping using single-cell RNA sequencing reveals principles and mechanisms of genetic interactions.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 16 Samples
FTP download: GEO (CSV, H5, MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133344/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA551220
Series		Accession: GSE133344	ID: 200133344

253. Discovering the anti-cancer potential of non-oncology drugs by systematic PRISM profiling
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133299/
Series		Accession: GSE133299	ID: 200133299

254. Transcriptional profiling of LS1034 cells treated with tepoxalin
(Submitter supplied) LS1034 colorectal cancer cells were treated with DMSO vehicle control or 12 uM tepoxalin for 6 hours. Anti-cancer uses of non-oncology drugs have been found on occasion, but such discoveries have been serendipitous and rare. To fully discover activity against multiple tumor types, resource-intensive screening across hundreds of cancer cell lines is needed. We sought to create a public resource containing the growth inhibitory activity of 4,518 drugs tested across 578 human cancer cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133286/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA550993
Series		Accession: GSE133286	ID: 200133286

255. Transcriptional profiling of SF295 cells following MTF1 knockout by CRISPR/Cas9
(Submitter supplied) SF295 glioblastoma cells were subjected to CRISPR/Cas9-mediated knockout of the MTF1 (metal regulatory transcription factor 1) gene or non-targeted control (GFP). Two guides targeting MTF1 and one guide targeting GFP were cloned into the pXPR_023 all-in-one CRISPR/Cas9 vector. SF295 cells were transduced by lentiviral infection and selected using puromycin. Following selection, RNA was harvested from cell lines growing in culture. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133285/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA550994
Series		Accession: GSE133285	ID: 200133285

256. PNET animal model: new insights (II)
(Submitter supplied) We studied our CNS-PNET animal model to get new insights on the onset of tumor formation
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85340/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338230
Series		Accession: GSE85340	ID: 200085340

257. Expression profiling of colorectal cancer cell lines
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.  These data are associated with single-cell RNA-seq data available at SRA at accession: SRP217361
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL570 34 Samples
FTP download: GEO (CEL, CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135461/
Series		Accession: GSE135461	ID: 200135461

258. Colorectal cancer cell lines with SETDB1 depletion [RNA-seq]
(Submitter supplied) We performed RNA sequencing analysis of three colorectal cancer cell lines (Caco2, HCT116, SW480) with SETDB1 knockdown. Samples were obtained after flow cytometry sorting according to KRT20 expression level.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135460/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA558968
Series		Accession: GSE135460	ID: 200135460

259. Tet inactivation disrupts YY1 binding and long-range chromatin interactions to cause developmental defects in embryonic heart
(Submitter supplied) Tet-mediated DNA methylation oxidation plays an important role in shaping the epigenetic landscapes and chromatin accessibility during gene expression. While several studies demonstrated pivotal roles of Tet proteins in regulating embryonic development, little is known about their functions in heart development. Here we systemetically analyzed DNA methylation and hydroxymethylation dynamics during early cardiac development in both human and mice. more...
Organism:	Homo sapiens; Mus musculus
Type:		Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
Platforms: GPL18573 GPL19057 23 Samples
FTP download: GEO (BW, HIC, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121671/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA505309
Series		Accession: GSE121671	ID: 200121671

260. Investigation of bivalently marked promoters in patient-derived colorectal cancer stem cells by ChIP-seq, chromatin accessibility by ATAC-seq, and differential regulation of gene expression following EZH2 inhibition using RNA-seq.
(Submitter supplied) We profiled changes in gene expression following EZH2 inhibition, in a patient-derived, cancer stem cell enriched model. Cells were treated with UNC1999, an EZH2 inhibitor, for 7 days, prior to processing for RNA-seq. In parallel, we identified H3K27me3 and H3K4me3 marked promoters using ChIP-seq at baseline in the same model, as well as chromatin accessibility using ATAC-seq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 13 Samples
FTP download: GEO (BROADPEAK, CSV, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113176/
Series		Accession: GSE113176	ID: 200113176

261. TAE sensitive and resistant Kelly cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing
4 related Platforms 118 Samples
FTP download: GEO (BEDPE, CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103084/
Series		Accession: GSE103084	ID: 200103084

262. Gene expression profiling of leukemia cells following asparagine depletion
(Submitter supplied) We will report the gene expression changes following asparagine depletion in human ALL cell line, RS4;11
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135420/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA558797
Series		Accession: GSE135420	ID: 200135420

263. Zika Virus Noncoding sfRNA Sequesters Multiple RNA Binding Proteins and Impacts mRNA Decay and Splicing
(Submitter supplied) Previous reports studying similar flavivirus infections (DENV, WNV, etc.) revealed an increase in both the abundance and stability of normally short-lived cellular mRNAs. This resulted from the stalling/repression of the major 5’-3’ host exoribonuclease XRN-1 on three-helix junction structures present in the 3’-UTR of insect-borne flaviviruses.   Therefore we sought to identify the endogenous mRNA abundance and stability changes induced during early and late times following Zika virus infection (PRBRAC59) in human choriocarcinoma (JAR) cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 5 Samples
FTP download: GEO (BED, FASTA, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135413/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA558783
Series		Accession: GSE135413	ID: 200135413

264. Global gene expression of mesenchymal like lung cancer cell (TD) induced by TGFb with control (A549)
(Submitter supplied) Analysis of TGF-β induced mesenchymal type of lung cancer compared with control A549 lung cancer cell at gene expression level. In order to investigate the characteristics of mesenchymal like lung cancer cell, we established mesenchymal type of lung cancer cell (TD) with chronic exposure with TGF-β. After we established TD cell line, RNA-seq was performed with total RNA extracted from TD and parental A549 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135402/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA558762
Series		Accession: GSE135402	ID: 200135402

265. ChIP-seq of p63 and RNA-seq of knockdown and overexpression of p63
(Submitter supplied) We performed ChIP-seq of p63 in ME-180 cell line and RNA-seq of knockdown and overexpression of p63
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135257/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA558077
Series		Accession: GSE135257	ID: 200135257

266. Modeling Human Cancer-induced Cachexia (Human)
(Submitter supplied) Cachexia is a wasting syndrome characterized by pronounced skeletal muscle loss.  In cancer, cachexia associates with increased morbidity and mortality and decreased treatment tolerance. Although advances have been made in understanding the mechanisms of cachexia, translating these advances to the clinic has been challenging. One reason for this shortcoming may be the current animal models that fail to fully recapitulate the etiology of human cancer-induced tissue wasting. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 10 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133523/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA551683
Series		Accession: GSE133523	ID: 200133523

267. Hierarchy of mono- and bi-allelic TP53 alterations in Multiple Myeloma cell fitness
(Submitter supplied) Comparison of the TP53 wild-type myeloma cell line AMO1 with the CRISPR/Cas9 engineered AMO1 cell line named UMC901. UMC901 harbors bi-allelic alterations to TP53:  TP53 del/mut. Analysis of impact of TP53 alterations on gene transcription and identification of affected pathways by transcriptome-wide differential gene expression analysis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132340/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA547633
Series		Accession: GSE132340	ID: 200132340

268. Bulk (100cell) RNA-Sequencing of human fetal haematopoietic stem, progenitor and B cells
(Submitter supplied) Human lymphopoiesis is a dynamic life-long process that starts in utero at 6 weeks gestation; however developmental pathways defining fetal lymphopoiesis are largely unexplored. While the first committed B-progenitor in normal human bone marrow (BM) is a CD10+ve ProB-progenitor, the identification of a CD10-ve B-progenitor (Pre/ProB progenitor) in cord blood suggests there may be a second B-lymphoid development program in fetal life. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 21 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122982/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA507127
Series		Accession: GSE122982	ID: 200122982

269. TCR repertoire and transcriptomic analyses of advanced solid tumors in first-in-human phase 1 study of IT1208, a defucosylated humanized anti-CD4 depleting antibody
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17303 GPL23934 124 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120102/
Series		Accession: GSE120102	ID: 200120102

270. T-cell receptor repertoire analysis of advanced solid tumors in first-in-human phase 1 study of IT1208, a defucosylated humanized anti-CD4 depleting antibody [TCR-seq]
(Submitter supplied) Immune checkpoint inhibitors such as anti-cytotoxic T-lymphocyte–associated antigen-4 and anti-programmed cell death-1 monoclonal antibodies (mAbs) agents or these combinations has improved outcomes of various cancers.However, still not a few patients fail to achieve clinical benefit, this highlights the importance of additional treatment to overcome its resistance. Previously, we showed that administration of the anti-CD4 mAb alone had strong anti-tumor effects that were superior to those elicited by CD25+ Treg depletion or other immune checkpoint mAbs in B16F10, Colon 26, or Lewis lung carcinoma subcutaneous tumor models. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL23934 GPL17303 105 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120101/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA491658
Series		Accession: GSE120101	ID: 200120101

271. Transcriptomic analysis of advanced solid tumors in first-in-human phase 1 study of IT1208, a defucosylated humanized anti-CD4 depleting antibody  [3'SAGE-seq]
(Submitter supplied) Immune checkpoint inhibitors such as anti-cytotoxic T-lymphocyte–associated antigen-4 and anti-programmed cell death-1 monoclonal antibodies (mAbs) agents or these combinations has improved outcomes of various cancers.However, still not a few patients fail to achieve clinical benefit, this highlights the importance of additional treatment to overcome its resistance. Previously, we showed that administration of the anti-CD4 mAb alone had strong anti-tumor effects that were superior to those elicited by CD25+ Treg depletion or other immune checkpoint mAbs in B16F10, Colon 26, or Lewis lung carcinoma subcutaneous tumor models. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 19 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120028/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA491654
Series		Accession: GSE120028	ID: 200120028

272. Grainyhead-like 2 (GRHL2) and epigenetic remodeling in the intermediate states of epithelial-mesenchymal transition
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Methylation profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL13534 GPL18573 GPL6244 166 Samples
FTP download: GEO (BW, CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118408/
Series		Accession: GSE118408	ID: 200118408

273. Grainyhead-like 2 (GRHL2) and epigenetic remodeling in the intermediate states of epithelial-mesenchymal transition [RNA-seq]
(Submitter supplied) Ovarian cancer (OC) cells exhibit varying extents of epithelial/mesenchymal phenotype, forming an EMT spectrum based on their EMT scores. Combining 450K DNA methylation array, ChIP-sequencing of five histone H3 marks (H3K4me1, H3K4me3, H3K27Ac, H3K27me3 and H3K9me3) and transcriptomic analyses, we examined the genome-wide epigenetic profiles of OC cell lines with progressive EMT phenotypes, including a knockdown model of EMT suppressor Grainyhead-like 2 (GRHL2) which showed intermediate state transition. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118407/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485494
Series		Accession: GSE118407	ID: 200118407

274. Human Papillomavirus (HPV) genomic integration, expression and E6/E7 splicing patterns in cervical cancer associated with HPV16 or HPV18 infection
(Submitter supplied) Human papillomavirus (HPV) genome integration into the host genome, blocking E2 expression and leading to overexpression of E6 and E7 viral oncogenes, is considered a major step in cervical cancer development. In high-risk HPVs, E6 and E7 oncogenes are expressed as a bicistronic pre-mRNA, with alternative splicing producing the ultimate mRNAs required for E6 and E7 translation. Given the number of alternative donor and acceptor splicing sites, ten E6/E7 different alternative transcripts might be formed for HPV16 and three for HPV18, although only six isoforms have been previously reported for HPV16. more...
Organism:	Human papillomavirus type 18; Homo sapiens; Human papillomavirus type 16
Type:		Expression profiling by high throughput sequencing
Platforms: GPL22768 GPL22767 25 Samples
FTP download: GEO (FASTA, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE91nnn/GSE91065/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA356774
Series		Accession: GSE91065	ID: 200091065

275. The XPO1 inhibitor KPT-8602 synergizes with dexamethasone for the inhibition of acute lymphoblastic leukemia
(Submitter supplied) Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer. Survival of ALL patients has improved significantly over the last 50 years. However, the current intensified chemotherapy is associated with serious short and long-term side effects in these young patients. Whereas KPT-8602 is a second generation exportin-1 (XPO-1) inhibitor with potent activity against ALL in pre-clinical models and with minimal effects on normal cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL20301 32 Samples
FTP download: GEO (BEDGRAPH, NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135350/
Series		Accession: GSE135350	ID: 200135350

276. Transcriptome analysis of A549 cells expressing a SUMOylation-deficient TRIM28 mutant in the context of influenza A virus infection
(Submitter supplied) Aim: Identify differentially expressed genes in human lung epithelial cells expressing a SUMOylation-deficient TRIM28 mutant (TRIM28 6KR) compared to TRIM28 wt.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133329/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA551131
Series		Accession: GSE133329	ID: 200133329

277. Nuclear receptor RORγ is a targetable master regulator of cholesterol in a subtype of breast cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL9052 GPL11154 23 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131857/
Series		Accession: GSE131857	ID: 200131857

278. Nuclear receptor RORγ is a targetable master regulator of cholesterol in a subtype of breast cancer [RNA-Seq]
(Submitter supplied) We show that triple-negative breast cancer (TNBC) exhibits a hyper-activated MVA-CB program that is strongly linked to nuclear receptor RORγ, compared to estrogen receptor-positive breast cancer. Genetic and pharmacological inhibition of RORγ reduces tumor cholesterol contents and synthesis rate while preserving host cholesterol homeostasis. We demonstrate, for the first time, that RORγ functions as a master activator of the entire MVA-CB program, dominantly over SREBP2, through its own direct binding and facilitating the recruitment of SREBP2. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131856/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA545131
Series		Accession: GSE131856	ID: 200131856

279. Dynamic 3D chromosomal landscapes in acute leukemia
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
4 related Platforms 61 Samples
FTP download: GEO (BED, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115896/
Series		Accession: GSE115896	ID: 200115896

280. Dynamic 3D chromosomal landscapes in acute leukemia [RNA-Seq]
(Submitter supplied) Background: Disruptions of 3D chromatin architecture can alter the activity of topologically associated domains (TADs), rewire enhancer-promoter interactions and thus significantly impact gene regulatory programs. Recently, such disruptions have been implicated in tumorigenesis, highlighting the need for a deeper understanding of their detailed role. Methods: T-ALL primary samples and prototypical cell lines as well as healthy T cell counterparts were profiled by in-situ Hi-C, RNA-Seq and CTCF ChIP-Seq. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL18573 9 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115895/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476372
Series		Accession: GSE115895	ID: 200115895

281. Dynamic gene expression in T-ALL following treatment and release of gamma-secretase inhibition [GRO-Seq]
(Submitter supplied) Gro-seq analysis following NOTCH1 inhibition and release gave an ovierview of the kinetics of NOTCH1 dependent transcriptional regulatiion
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 20 Samples
FTP download: GEO (BW, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115894/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476373
Series		Accession: GSE115894	ID: 200115894

282. DNA methylation loss coupled with mitotic cell division promotes immune evasion of tumours with high mutation load [RNA-seq]
(Submitter supplied) Mitotic cell division increases tumour mutation burden and copy number load, predictive markers of the clinical benefit of immunotherapy. Cell division correlates also with genomic demethylation involving methylation loss in late-replicating partial methylation domains. Here we find that immunomodulatory pathway genes are concentrated in these domains and transcriptionally repressed in demethylated tumours with CpG island promoter hypermethylation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 27 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135222/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA557841
Series		Accession: GSE135222	ID: 200135222

283. Proline 152 mutation in p53 abolishes cognate DNA binding, induces gain of function tumorigenesis
(Submitter supplied) We have identified a relatively rare mutation in p53 in an Indian oral cancer patient sample at the fade end of its DNA binding domain [P152L]. Although P152L p53 DBD potentially binds to DNA, the full length protein is completely devoid of cognate site DNA binding ability. Also the mutant protein can efficiently tetramerize. Significantly, this mutant was found to induce cell mobility and proliferation with greater tumorigenic potential in nude mice, the mechanistic details of which is also investigated upon. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119654/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489860
Series		Accession: GSE119654	ID: 200119654

284. transcriptome expression profiling of cisplatin chemoresistance 5-8F cells
(Submitter supplied) Radiotherapy and adjuvant cisplatin (DDP) chemotherapy are standard administrations applied in the treatment of NPC. However, molecular change and functions of DDP chemo-resistance in nasopharyngeal carcinoma are still poorly understood.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135083/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA557360
Series		Accession: GSE135083	ID: 200135083

285. Transcriptomic data and Genome-wide maps of chromatin state in prostate cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL20301 GPL23479 GPL21290 14 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131830/
Series		Accession: GSE131830	ID: 200131830

286. Paxillin regulates genomic networks in prostate cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 30 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131731/
Series		Accession: GSE131731	ID: 200131731

287. Paxillin regulates genomic networks in prostate cancer [PC3]
(Submitter supplied) We report that the adaptor protein, paxillin, regulates some proliferative and apoptotic genes in the castration resistant prostate cancer cell line, PC3.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131730/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA544534
Series		Accession: GSE131730	ID: 200131730

288. Paxillin regulates genomic networks in prostate cancer [C4-2]
(Submitter supplied) We report that the adaptor protein, paxillin, regulates some androgen responsive genes in the castration resistant prostate cancer cell line,C4-2.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131728/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA544528
Series		Accession: GSE131728	ID: 200131728

289. Paxillin regulates genomic networks in prostate cancer [LNCaP]
(Submitter supplied) We report that the adaptor protein, paxillin, regulates some androgen responsive genes in the castration sensitive prostate cancer cell line, LNCaP.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131726/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA544525
Series		Accession: GSE131726	ID: 200131726

290. A pliable mediator acts as a functional, rather than an architectural bridge, between promoters and enhancers
(Submitter supplied) Our mechanistic understanding of Mediator derives largely from studies of the 25-subunit yeast complex. Here we combine CRISPR-Cas9 genetic screens, degron assays, in situ Hi-C, and cryo-EM to dissect the function and structure of the 33-subunit mammalian Mediator (mMED). Deletion analyses in B, T and ES cells reveal that depletion of the entire complex blocks PolII recruitment genome-wide, while loss of non-essential subunits, including the Tail module, primarily affects promoters linked to multiple enhancers. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
6 related Platforms 201 Samples
FTP download: GEO (BEDGRAPH, BW, HIC, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121355/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497125
Series		Accession: GSE121355	ID: 200121355

291. Dissecting polymerase pausing with TV-PRO-seq
(Submitter supplied) Transcription of many genes in metazoans is subject to polymerase pausing, which corresponds to the transient arrest of transcriptionally engaged polymerase. It occurs mainly at promoter proximal regions and is not well understood. In particular, a genome-wide measurement of pausing times at high resolution has been lacking. This is because relevant experimental techniques are mostly based on average polymerase occupancies across many cells which cannot discriminate between few slow polymerases and many quick polymerases at a position, since the data corresponds to the average of many cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 20 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118957/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487532
Series		Accession: GSE118957	ID: 200118957

292. Unr is a potential post-transcriptional master regulator of protein expression
(Submitter supplied) Ribonucleoprotein immunoprecipitation followed by mass spectrometry and RNA-Seq was used to investigate the ‘Upstream of N-RAS’ (UNR) protein interactome across three cancer cell lines. A number of novel UNR-interacting proteins and transcripts were discovered, including the ubiquitin E3 ligase, HUWE1; the nucleolar protein, NARR; the multifunctional protein, SQSTM1; and the erythropoiesis-related protein, LDB1 . more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 36 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118279/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485061
Series		Accession: GSE118279	ID: 200118279

293. Preliminary RNA-seq data obtained from H1975 and H661 cells exposed to AAT protein
(Submitter supplied) Although the classical function of AAT is to inhibit neutrophil proteases, there is evidence that the role of AAT in inflammation is multifaceted. AAT possesses anti-inflammatory activity against immune cells, affects leukotriene B4, TNF-α, IL-8, IFN-γ and IL-1β production and expresses potent anti-apoptotic properties. In addition, AAT has been shown to inhibit the activity of natural killer cells against tumor cells, which indicates that AAT may play multiple functions during cancer development. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135138/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA557498
Series		Accession: GSE135138	ID: 200135138

294. RNA-SEQ of humna lung and breast cancer cell lines
(Submitter supplied) We cultured human lung and breast cancer cell lines, A549, H23, MDA-MB-231, MCF-7-TNR, and T47D cells. Total RNA was extracted and processed for RNA-SEQ.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135112/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA557456
Series		Accession: GSE135112	ID: 200135112

295. Genome-wide analysis of Ctr and OPA1 knock-down transcriptomes
(Submitter supplied) Through the genome-wide analysis of Ctr and OPA1 knock-down group, we reveal the transcriptome changes with OPA1 down-regulation
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135089/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA557415
Series		Accession: GSE135089	ID: 200135089

296. RNA-seq analysis of A498 cell line treated with siSETD2 or si-NC
(Submitter supplied) the coordinated expression of SETD2-miRNAs-MAPK/JNK may be predictive of poor prognostic in patients with RCC. Our findings also emphasize the therapeutic potential of MAP4K4 in RCC therapy and support the development of an effective therapeutic strategy to target MAP4K4 by molecularly targeted approaches.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133521/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA551678
Series		Accession: GSE133521	ID: 200133521

297. Next generation sequencing analysis of transcriptomes in MDA-MB-231 and LM2-4175 cell lines
(Submitter supplied) LM2-4175 cell line was originally selected from MDA-MB-231,but has more aggressive characteristics in invasion, migration and metastasis. In addition, LM2 cell line specifically metastasizes to lung. To understand the melecular mechanisms of lung metastasis in breast cancer,we analyzed the RNA-seq data of MDA-MB-231 and LM2-4175 cell lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124380/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA511878
Series		Accession: GSE124380	ID: 200124380

298. Dualism of FGF and TGFb signaling in activation of heterogeneous cancer-associated fibroblast populations converging on cancer development
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL16791 GPL23126 GPL11154 91 Samples
FTP download: GEO (CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122372/
Series		Accession: GSE122372	ID: 200122372

299. Dualism of FGF and TGFb signaling in activation of heterogeneous cancer-associated fibroblast populations converging on cancer development (RNA-Seq_65_HDF)
(Submitter supplied) The molecular basis for heterogeneity of cancer-associated fibroblast (CAF) populations remains to be established. We report that fibroblast growth factor (FGF) and transforming growth factor-beta (TGFB) signaling are strong opposite modulators of key CAF effector genes. While FGF activation in normal human dermal fibroblasts (HDFs) induces a number of mitogenic growth factors and metalloproteases, it suppresses expression of pro-fibrotic and cancer-associated extracellular matrix proteins, with TGFB exerting reverse effects. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 65 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122369/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA504811
Series		Accession: GSE122369	ID: 200122369

300. Dualism of FGF and TGFb signaling in activation of heterogeneous cancer-associated fibroblast populations converging on cancer development (RNA-Seq_FGF2)
(Submitter supplied) The molecular basis for heterogeneity of cancer-associated fibroblast (CAF) populations remains to be established. We report that fibroblast growth factor (FGF) and transforming growth factor-beta (TGFB) signaling are strong opposite modulators of key CAF effector genes. While FGF activation in normal human dermal fibroblasts (HDFs) induces a number of mitogenic growth factors and metalloproteases, it suppresses expression of pro-fibrotic and cancer-associated extracellular matrix proteins, with TGFB exerting reverse effects. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122368/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA504810
Series		Accession: GSE122368	ID: 200122368

301. Activation of PARP-1 by snoRNAs Controls Ribosome Biogenesis and Cell Growth via the RNA Helicase DDX21
(Submitter supplied) PARP inhibitors (PARPi) are thought to control cancer cell growth by inducing synthetic lethality with DNA repair defects (e.g., in BRCA1/2 mutant cells). We have identified an alternate pathway for PARPi-mediated growth control in BRCA1/2-intact breast cancer cells involving rDNA transcription and ribosome biogenesis. PARP-1 binds to snoRNAs, which stimulate PARP-1 catalytic activity in the nucleolus independent of DNA damage. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 14 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115761/
Series		Accession: GSE115761	ID: 200115761

302. Activation of PARP-1 by snoRNAs Controls Ribosome Biogenesis and Cell Growth via the RNA Helicase DDX21 (RNA-Seq)
(Submitter supplied) PARP inhibitors (PARPi) prevent cancer cell growth by inducing synthetic lethality with DNA repair defects (e.g., in BRCA1/2 mutant cells). We have identified an alternate pathway for PARPi-mediated growth control in BRCA1/2-intact breast cancer cells involving rDNA transcription and ribosome biogenesis. PARP-1 binds to snoRNAs, which stimulate PARP-1 catalytic activity in the nucleolus independent of DNA damage. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (BW, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115760/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475966
Series		Accession: GSE115760	ID: 200115760

303. CD97 is a Critical Regulator of Acute Myeloid Leukemia Stem Cell Function
(Submitter supplied) Despite significant efforts to improve therapies for acute myeloid leukemia (AML), clinical outcomes remain poor. Understanding the mechanisms that regulate the development and maintenance of leukemic stem cells (LSC) is important to reveal new therapeutic opportunities. We have identified CD97, a member of the adhesion class of G-protein coupled receptors (GPCRs), as a frequently upregulated antigen of AML blasts that is a critical regulator of blast function. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135028/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA557192
Series		Accession: GSE135028	ID: 200135028

304. A tumor specific super-enhancer drives immune evasion by guiding synchronous expression of PD-L1 and PD-L2
(Submitter supplied) A tumor specific super-enhancer drives immune evasion by guiding synchronous expression of PD-L1 and PD-L2
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 2 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135016/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA557163
Series		Accession: GSE135016	ID: 200135016

305. Epigenomics and Single-cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis [scRNA-seq]
(Submitter supplied) Langerhans cell histiocytosis (LCH) is a rare neoplasm predominantly affecting children. It occupies a characteristic hybrid position between cancers and inflammatory diseases, which makes it an attractive model for studying cancer development. To explore the molecular mechanisms underlying the pathophysiology of LCH and its characteristic clinical heterogeneity, we investigated the transcriptomic and epigenomic diversity in primary LCH lesions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 7 Samples
FTP download: GEO (H5) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133704/
Series		Accession: GSE133704	ID: 200133704

306. Enhancement of Human B Cell Differentiation and Function in Lymph Nodes by the TLR9 Agonist MGN1703
(Submitter supplied) TLR9 agonists are being developed as immunotherapies to increase immune effector cell activity against malignancies and pathogens. However, the in vivo impacts of TLR9 agonism on human B cells are incompletely known and the impacts of such treatments on human lymph node B cells are unknown. These are major knowledge gaps given the high TLR9 expression levels in B cells and the importance of lymph nodes for B cell activity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130307/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA535447
Series		Accession: GSE130307	ID: 200130307

307. Couple transcriptome and genomic data obtained from the PDXs to identify pathways linking oncogenic alterations
(Submitter supplied) Purpose: Study  the changes in cell transcriptome in breast cancer with respect to normal breast tissue in association with somatic mutations Methods: RNA was extracted from frozen normal breast tissues and PDXs cells Results: We found over-expression of oncogenic pathways associated with oncogenic mutations in PDXs
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 21 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129563/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA531824
Series		Accession: GSE129563	ID: 200129563

308. Insulin induced alterations in chromatin acetylation and transcriptome in triple negative breast cancer cells
(Submitter supplied) We have performed quantitative H3K9ac ChIP-seq and RNA-seq from untreated and 3h, 6h insulin treated MDA-MB-231 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124127/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510812
Series		Accession: GSE124127	ID: 200124127

309. Single cell RNA-seq analysis of medulloblastoma
(Submitter supplied) Medulloblastoma is a malignant childhood cerebellar tumour comprised of distinct molecular subgroups. Whereas genomic characteristics of these subgroups are well defined, the extent to which cellular diversity underlies their divergent biology and clinical behaviour remains largely unexplored. We used single-cell transcriptomics to investigate intra- and inter-tumoural heterogeneity in twenty-five medulloblastomas spanning all molecular subgroups. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119926/
Series		Accession: GSE119926	ID: 200119926

310. The p30 isoform of CEBPA uncovers a silent enhancer to drive the expression of the tumor promotive factor CD73 in CEBPA mutant AML
(Submitter supplied) CEBPA is a key hematopoietic transcription factor (TF), found mutated in 5-14% of all acute myeloid leukemia (AML) cases, but the direct molecular ramifications of this driver mutation remains elusive. To investigate CEBPA-mutant AML, we compared patient aberrant genetic programs with changes in a precise mouse model (Lp30) expressing only the cancer-prevalent truncated CEBPA, p30, and identified a stringent cross-species AML program. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL19057 GPL11154 GPL13112 35 Samples
FTP download: GEO (BW, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118963/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487543
Series		Accession: GSE118963	ID: 200118963

311. T cell and Monocyte Specific RNAseq Analysis in Septic and Non Septic Critically-Ill Patients and in Patients with Cancer
(Submitter supplied) The purpose of this study was to determine the potential differential effect of sepsis on innate versus adaptive immune effector cells by examining RNA expression in monocyte/macrophages and CD4 and CD8 T cells respectively using next generation sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 231 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133822/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA552599
Series		Accession: GSE133822	ID: 200133822

312. Mesenchymal stem/stromal cell engulfment reveals metastatic advantage in breast cancer
(Submitter supplied) We isolated the engulfing MDA-MB-231 breast cancer cells and would like to see the differences as compared to WT
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 9 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131011/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA542295
Series		Accession: GSE131011	ID: 200131011

313. HMGA1 and FOXM1 synergistically regulate a common gene network modulating angiogenesis in breast cancer
(Submitter supplied) One of the factors involved in TNBC aggressiveness is HMGA1, a member of non-histone chromatin proteins. The High mobility group A1 is an architectural transcription factor which, by altering chromatin structure and interacting with transcription factors, can regulate the transcription of several genes. HMGA1 protein is defined as an oncofetal protein as it is highly expressed during the embryogenesis while its expression decreases or is absent in adults, and it is re-expressed in a variety of tumors, including breast cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129915/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA533135
Series		Accession: GSE129915	ID: 200129915

314. Overexpression of UGT2B17 in MEC1 and JVM2 leukemia cell lines
(Submitter supplied) UGT2B17 is a recently identified molecular marker for poor prognosis in Chronic Lymphocytic Leukemia (CLL), which is the most prevalent adult leukemia subtype in the western world. The goal of this study was to determine the effects of UGT2B17 expression in leukemia cells and to find molecular pathways associated with high UGT2B17 expression. We characterized the effects of UGT2B17 in two leukemia cell lines (MEC1 and JVM2) overexpressing a functional UGT2B17 enzyme. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121626/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497889
Series		Accession: GSE121626	ID: 200121626

315. Characterization of Human Pegivirus Infection in Liver Transplantation Recipients
(Submitter supplied) Approximately 2% of heathy persons are infected with human pegivirus (HPgV). HPgV is transmitted via vertical, sexual, and blood-borne routes. Recently, the association of HPgV infection with the risk of lymphoma was reported. We examined the prevalence of chronic HPgV infection in liver transplantation (LT) recipients and hepatectomy patients and the influence of HPgV infection after LT on clinical and perioperative factors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131504/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA543863
Series		Accession: GSE131504	ID: 200131504

316. Genome-wide identification of transcripts associated with KIAA1429 by RIP-seq
(Submitter supplied) N6-methyladenosine (m6A) modification, as the most abundant internal methylation of eukaryotic RNA transcripts, is critically implicated in RNA processing, decay, transport and translation. Here we showed that KIAA1429, the largest known component in the m6A methyltransferase complex, was considerably upregulated in hepatocellular carcinoma (HCC) tissues. High expression of KIAA1429 was significantly associated with the malignant clinical features and the poor prognosis of HCC patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134978/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA556906
Series		Accession: GSE134978	ID: 200134978

317. Estrogen deprivation triggers and immunosuppressive phenotype in breast cancer cells
(Submitter supplied) Our study reveals that while antiestrogen therapies effectively limit tumor growth in ER-positive breast cancers, they also trigger a transcriptional program that favors immune evasion.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 9 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134938/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA556857
Series		Accession: GSE134938	ID: 200134938

318. RNA sequencing of MCF-7 cells transfected with non-specific or DAXX specific siRNA
(Submitter supplied) Purpose: to determine what genes require DAXX for their regulation in ER+ breast cancer cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134919/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA556808
Series		Accession: GSE134919	ID: 200134919

319. NHLRC1 re-expression in cancer cells
(Submitter supplied) Flag-tagged NHLRC1 expression in three different cancer cell lines
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132776/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA548954
Series		Accession: GSE132776	ID: 200132776

320. Induced pluripotent stem cell modeling of bone marrow failure and MDS identifies therapeutic targets
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118378/
Series		Accession: GSE118378	ID: 200118378

321. The effect of spontaneous acquisition of an extra chromosome 7 for engineered del(7q) on induced pluripotent stem cells (iPSCs) derived from patients with Shwachman Diamond Syndrome (SDS).
(Submitter supplied) Monosomy 7 or deletion of 7q (del(7q)) frequently arise in inherited and acquired bone marrow failure, and are associated with progression to high grade Myelodysplastic Syndrome (MDS) and acute leukemia.  Current non-transplant approaches to treat marrow failure may be complicated by potential stimulation of clonal outgrowth.  To study the biological consequences of del(7q) within the context of a failing marrow, we utilized induced pluripotent stem cells (iPSCs) derived from patients with Shwachman Diamond Syndrome (SDS) and genomically engineered a deletion of (7q). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118377/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485358
Series		Accession: GSE118377	ID: 200118377

322. The effect of engineered del(7q) on induced pluripotent stem cells (iPSCs) derived from patients with Shwachman Diamond Syndrome (SDS).
(Submitter supplied) Monosomy 7 or deletion of 7q (del(7q)) frequently arise in inherited and acquired bone marrow failure, and are associated with progression to high grade Myelodysplastic Syndrome (MDS) and acute leukemia.  Current non-transplant approaches to treat marrow failure may be complicated by potential stimulation of clonal outgrowth.  To study the biological consequences of del(7q) within the context of a failing marrow, we utilized induced pluripotent stem cells (iPSCs) derived from patients with Shwachman Diamond Syndrome (SDS) and genomically engineered a deletion of (7q). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118372/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485349
Series		Accession: GSE118372	ID: 200118372

323. Promoter activity profiling reveals on- and off-target transcriptional responses to drug treatment
(Submitter supplied) Owing to safety concerns or insufficient potential for efficacy, only 0.01% to 0.02% of new drug candidates are approved for marketing. Drugs already on the market may be withdrawn or restricted to certain uses due to adverse effects (AEs) discovered after market introduction. Comprehensively investigating the on-/off-target effects of drugs can help expose AEs during the drug development process. In this study, we developed an integrative framework for systematic identification of on-/off-target pathways and elucidation of the underlying mechanisms, by combining expression profiling after drug treatment with gene perturbation of the primary drug target. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 180 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134817/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA556524
Series		Accession: GSE134817	ID: 200134817

324. Gene expression profiling for HCCLM3 cells with shCtrl or shKIAA1429
(Submitter supplied) N6-methyladenosine (m6A) modification, as the most abundant internal methylation of eukaryotic RNA transcripts, is critically implicated in RNA processing, decay, transport and translation. Here we showed that KIAA1429, the largest known component in the m6A methyltransferase complex, was considerably upregulated in hepatocellular carcinoma (HCC) tissues. High expression of KIAA1429 was significantly associated with the malignant clinical features and the poor prognosis of HCC patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134776/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA556402
Series		Accession: GSE134776	ID: 200134776

325. C/EBPa mediates the growth inhibitory effect of progestins on breast cancer cells
(Submitter supplied) Steroid hormones are key gene regulators in breast cancer cells. While estrogens stimulate cell proliferation, progestins activate a single cell cycle followed by proliferation arrest. Here, we use biochemical and genome wide approaches to show that progestins achieve this effect via a functional crosstalk with C/EBPα. Using ChIP-seq, we identify around 1,000 sites where C/EBPα binding precedes and helps binding of Progesterone Receptor (PR) in response to hormone. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL9052 30 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132649/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA548573
Series		Accession: GSE132649	ID: 200132649

326. Modeling the MYC-driven normal-to-tumour switch in breast cancer.
(Submitter supplied) The potent MYC oncoprotein is deregulated in many human cancers, including breast carcinoma, and is associated with aggressive disease. To understand the mechanisms and vulnerabilities of MYC-driven breast cancer, we have generated an in vivo model that mimics human disease in response to MYC deregulation. MCF10A cells ectopically expressing a common breast cancer mutation in the PI3 kinase pathway (PIK3CAH1047R) lead to the development of organized acinar structures in mice. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (CSV, TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130513/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540502
Series		Accession: GSE130513	ID: 200130513

327. RNA-seq of breast cancer cell lines post ligand treatment II
(Submitter supplied) Goal: study the impact of estrogen receptor ligands on gene expression in HR+ breast cancer cells Methods: RNA sequencing Results: Ligand 4-OH tamoxifen, a selective ER modulator (SERM), promotes transcriptional activation of ER and mimics the transcriptional effect of natural ligand E2 for a subset of ER target genes, consistently across the seven breast cell lines (MDA-MB-134 VI, MDA-MB-330, EFM-19, T-47D, and BT-474). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 38 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128911/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529360
Series		Accession: GSE128911	ID: 200128911

328. ATAC-seq, ChIP-seq and RNA-seq of breast cancer cell lines post ligand treatment
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL20301 145 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117943/
Series		Accession: GSE117943	ID: 200117943

329. RNA-seq of breast cancer cell lines post ligand treatment I
(Submitter supplied) Goal: study the impact of estrogen receptor ligands on gene expression in HR+ breast cancer cells Methods: RNA sequencing Results: Ligand 4-OH tamoxifen, a selective ER modulator (SERM), promotes transcriptional activation of ER and mimics the transcriptional effect of natural ligand E2 for a subset of ER target genes, consistently across the seven breast cell lines (MCF-7, HCC1500, MDA-MB-330, EFM-19, T-47D, BT-474, and CAMA-1). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 82 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117942/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483773
Series		Accession: GSE117942	ID: 200117942

330. RNA-Sequencing of Transplant Stage Idiopathic Pulmonary Fibrosis Lung Reveals Unique Pathway Regulation
(Submitter supplied) We report an RNA-seq based transcriptomic fingerprint of severe IPF enriched in pathways of T-cell infiltration/activation, tumor development and cholesterol homeostasis. We highlight novel splice variants, candidate targets and biomarkers in advanced IPF.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 80 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134692/
Series		Accession: GSE134692	ID: 200134692

331. Cancer-Causing Mutations in SF3B1 Alter Splicing by Disrupting Interaction with SUGP1
(Submitter supplied) SF3B1, which encodes an essential spliceosomal protein, is frequently mutated in myelodysplastic syndromes (MDS) and many cancers. However, the defect of mutant SF3B1 is unknown. Here, we analyzed RNA-sequencing data from MDS patients and confirmed that SF3B1 mutants use aberrant 3' splice sites. To elucidate the underlying mechanism, we purified complexes containing either wild-type or the hotspot K700E mutant SF3B1, and found that levels of a poorly studied spliceosomal protein, SUGP1, were reduced in mutant spliceosomes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128805/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA528926
Series		Accession: GSE128805	ID: 200128805

332. The Liquid Liver Biopsy: Detection of Circulating Epithelial Cells in Liver Disease
(Submitter supplied) Using a microfluidic device, circulating epithelial cells (CECs) were enriched from peripheral blood from patients with chronlic liver disease and hepatocellular carcinoma. Select samples were further flow sorted for WBC subsets. CEC and WBC subsets transcriptomes were sequenced.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 137 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117623/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483004
Series		Accession: GSE117623	ID: 200117623

333. Characterisation of the EZH2 regulated transcriptome in de novo transformed cells (RNA-Seq)
(Submitter supplied) Epigenetic regulators are often hijacked by cancer cells to sustain and enhance their malignant phenotypes. Co-opted proteins are typically not mutated and their intrinsic properties remain unaltered. How cancer cells repurpose key regulators of cell identity as tumour-promoting factors is unclear. The antithetic role of the Polycomb component EZH2 in normal brain and glioma provides a paradigm to dissect how wild-type chromatin modifiers gain a pathological function in cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126395/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA521767
Series		Accession: GSE126395	ID: 200126395

334. Transcriptome-wide expression analyses of HCT116 cell line under 5 conditions
(Submitter supplied) Selective regulation of target genes by transcription factors is fundamental to cell-fate determination. The tumour suppressor p53, encoded by the most frequently mutated gene in human cancer, selectively regulates subsets of target genes in response to different cues. It remains poorly understood at the genomic level and structurally how p53 target selectivity is determined by cellular factors. Here we combine transcriptomic, chromatin binding and crystallographic studies to show that p53’s genome-wide discrimination between different sets of targets is influenced by its partner iASPP.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111798/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438163
Series		Accession: GSE111798	ID: 200111798

335. G0/G1 switch gene 2 modulates gliomagenesis and radiation response
(Submitter supplied) Glioblastoma multiforme (GBM), a WHO grade IV glioma is the most common and malignant primary cancer of the central nervous system with a grim median survival of 16 to 17 months upon diagnosis. Radiotherapy is the standard first line treatment for newly diagnosed patients with gliomas, but its effectiveness is limited given their intrinsic resistance and propensity for recurrence. Although possible mechanisms have been attributed to GBM resistance to radiation treatments, the molecular mechanisms regulating radiation resistance of GBM are still unclear.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86213/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA340944
Series		Accession: GSE86213	ID: 200086213

336. hCINAP regulates the DNA damage response and mediates the resistance of acute myelocytic leukemia cells to therapy
(Submitter supplied) Through RNA-seq of wildtype and hCINAP-deleted U2OS cells and whole genome bisulfite sequencing of the two U2OS cells, we show here that hCINAP is responsible for genomic stability and DNA damage response. Deletion of hCINAP directly decreased genomic stability and caused drug sensitivity. Also, when hCINAP is deleted, many genes are upregulated. These genes are involved in aging, DNA damage response and leukemia. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134342/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA554810
Series		Accession: GSE134342	ID: 200134342

337. Quantitative analysis of bi-modal binding of BET proteins at promoters predicts I-BET sensitivity
(Submitter supplied) We identified a chromatin displacement signature for the bromodomain proteins BRD2, BRD3 and BRD4 at TSS following treatment with I-BET152, an inhibitor of BET proteins. By integrating ChIP-seq, RNA-seq and Chem-seq data, we correlated alteration of the BRD4 signature at TSS with strong downregulation of gene expression which will facilitate identification of markers of sensitivity and resistance to drug.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform: GPL11154 88 Samples
FTP download: GEO (BED, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120715/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494237
Series		Accession: GSE120715	ID: 200120715

338. Hes1 is Associated with Long Non-Coding RNAs in Colorectal Cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Non-coding RNA profiling by array; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL16956 GPL16791 7 Samples
FTP download: GEO (TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134552/
Series		Accession: GSE134552	ID: 200134552

339. A kinase inhibitor screen identifies a dual cdc7/CDK9 inhibitor to sensitise triple-negative breast cancer to EGFR-targeted therapy
(Submitter supplied) Purpose: To investigate the impact of combined cdc7, CDK9 and EGFR inhibition on the transcriptomic profile of EGFR-TKI-resistant TNBC cells using high-throughput RNA sequencing. Methods: EGFR-TKI-resistant TNBC cell lines (Hs578T and SKBR7) were treated with DMSO, lapatinib (3.16 µM), PHA-767491 (1 µM) or co-treated with lapatinib (3.16 µM) & PHA-767491 (1 µM) for 6 hours. RNA was isolated with RNeasy Plus Mini Kit as described by manufacturer (QIAGEN, Cat. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131375/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA543423
Series		Accession: GSE131375	ID: 200131375

340. Heterozygous p53-R280T mutation promotes proliferation of NPC cells through activating PI3K/Akt signaling pathway
(Submitter supplied) Heterozygous p53-R280T mutations frequently occur in many nasopharyngeal carcinoma cell lines and nasopharyngeal carcinoma patients. However, the role of this mutation in the progression of nasopharyngeal carcinoma remains unclear. In this study, we successfully generated the tp53 knockout nasopharyngeal carcinoma (NPC) cells by CRISPR/Cas9-mediated genome editing and found that knockout of heterozygous tp53-R280T inhibited the proliferation of NPC cells significantly in vivo and in vitro. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130398/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA539983
Series		Accession: GSE130398	ID: 200130398

341. Targets of CDK12 on ZR-75-30 breast cancer cells (RNA-seq)
(Submitter supplied) RNA-sequencing analysis of CDK12 overexpressiong ZR-75-30 cell lines. Cyclin dependent kinase 12 (CDK12) is amplified in approximately 70-90% of HER2 amplified breast cancer. Results provide insight into the targets of CDK12 in HER2 positive breast cancer.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117523/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482401
Series		Accession: GSE117523	ID: 200117523

342. RNA-Seq on the effect of VitaminD on colonic and tumor organoids
(Submitter supplied) Stem cell enriched cultures are generated from primary cultures of colorectal cancer patients. Organoids from normal and tumoral tissue are treated with 1,25(OH)2D3 and vehicle for 96 hours. RNA expression is compared among treatments.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (CSV, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100785/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393037
Series		Accession: GSE100785	ID: 200100785

343. RNA-binding protein immunoprecipitation (RIP)and RNA sequencing
(Submitter supplied) We report the result of lncRNAs binding to Hes1 in colon cancer SW480 cells using Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore, MD, USA) following the manufacturer's instructions, the RNAs were analyzed by Illumina HiSeq 2500 Sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL16791 1 Sample
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134551/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA555809
Series		Accession: GSE134551	ID: 200134551

344. Dissecting the single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer [10x genomics]
(Submitter supplied) Intestinal-type gastric cancer is preceded by premalignant lesions including chronic atrophic gastritis and intestinal metaplasia. In this study, we performed a scRNA-seq survey of 56,440 cells from thirteen gastric antral mucosa biopsies from nine patients with Non-atrophic gastritis (NAG), CAG, IM or early gastric cancer (EGC), and constructed a single-cell transcriptome atlas for gastric premalignant and early-malignant lesions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134520/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA555477
Series		Accession: GSE134520	ID: 200134520

345. Effects of small molecules targeting the androgen receptor DNA-binding domain on prostate cancer cell transcriptome
(Submitter supplied) Prostate cancer is a leading cause of cancer related death among men. Current Androgen Receptor (AR) antagonists often target the ligand binding domain (LBD). However, occurrence of resistance to drugs targeting the LBD is common due to emergence of mutations in the LBD or constitutively active variants that lack the LBD itself.  Two novel small molecules, VPC-17005 and VPC-14449 targeting the DNA-binding domain have been developed and published previously. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127816/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA525448
Series		Accession: GSE127816	ID: 200127816

346. RNA-seq in SUNE-1 cells after downregulation of DANCR expression
(Submitter supplied) To explore whether DANCR plays a role in  nasopharyngeal carcinoma tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of DANCR siRNA and control groups.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117415/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482051
Series		Accession: GSE117415	ID: 200117415

347. Lineage tracing of acute myeloid leukemia reveals the impact of hypomethylating agents on chemoresistance selection
(Submitter supplied) Chemotherapy-resistant cancer recurrence is a major cause of mortality. In acute myeloid leukemia (AML), chemorefractory relapses result from the complex interplay between altered genetic, epigenetic and transcriptional states in leukemic cells. We developed an experimental model system using in vitro lineage tracing coupled with exome, transcriptome and in vivo functional readouts to assess the AML population dynamics and associated molecular determinants underpinning chemoresistance development. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134506/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA555350
Series		Accession: GSE134506	ID: 200134506

348. Downregulation of the histone methyltransferase SETD2 promotes imatinib resistance in chronic myeloid leukemia cells
(Submitter supplied) Epigenetic modifiers were important players in the development of hematological malignancies and sensitivity to therapy. Mutations of SET domain-containing 2 (SETD2), a methyltransferase that catalyzes the trimethylation of histone 3 on lysine 36 (H3K36me3), were found in various myeloid malignancies. However, the detailed mechanisms through which SETD2 confers chronic myeloid leukemia progression and resistance to therapy targeting on BCR-ABL remain unclear. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124894/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA514230
Series		Accession: GSE124894	ID: 200124894

349. GREB1, a novel target of Wnt signaling, promotes development of hepatoblastoma by suppressing TGFβ signaling
(Submitter supplied) The β-catenin mutation is frequently observed in hepatoblastoma (HB), but the underlying mechanism by which Wnt/β-catenin signaling induces HB tumor formation is unknown. We found that expression of growth regulation by estrogen in breast cancer 1 (GREB1) depends on Wnt/β-catenin signaling in HB patients. GREB1 was localized to the nucleus where it bound Smad2/3 in a competitive manner with p300 and inhibited TGFβ signaling, thereby promoting HepG2 HB cell proliferation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133976/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA553229
Series		Accession: GSE133976	ID: 200133976

350. Loss of CHD1 facilitates oncogenic hijacking of AR during cancer progression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 GPL20301 40 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117431/
Series		Accession: GSE117431	ID: 200117431

351. Loss of CHD1 facilitates oncogenic hijacking of AR during cancer progression [RNA-seq]
(Submitter supplied) Deregulation of chromatin architecture is emerging as a critical feature of carcinogenesis, and genomic alterations in nucleosome remodelers are common in human cancer. Recurrent deletion of the chromatin remodeler CHD1 is among the most common alterations in prostate cancer, but its role as a tumor suppressor and the reasons for the tissue-specific nature of CHD1 deletion remain undefined. Here, we show that deletion of CHD1 drives prostate tumorigenesis and fundamentally reprograms the transcriptional program of the androgen receptor (AR), diverting AR towards an oncogenic transcriptional program and away from a growth suppressive transcriptome. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117429/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482106
Series		Accession: GSE117429	ID: 200117429

352. The Polycomb Repressor Complex 1 Drives Double-Negative Prostate Cancer Metastasis by Coordinating Stemness and Immune Suppression
(Submitter supplied) The mechanisms that enable immune evasion at metastatic sites are poorly understood. We show that the Polycomb Repressor Complex 1 (PRC1) drives colonization of the bones and visceral organs in double-negative prostate cancer (DNPC). In vivo genetic screening identifies CCL2 as the top prometastatic gene induced by PRC1. CCL2 governs self-renewal and induces the recruitment of M2-like tumor-associated macrophages and regulatory T cells, thus coordinating metastasis initiation with immune suppression and neoangiogenesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103074/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA400081
Series		Accession: GSE103074	ID: 200103074

353. Multi-omics profiling reveals key signaling pathways in ovarian cancer controlled by STAT3
(Submitter supplied) Inhibiting STAT3 signaling reduces tumor progression, metastases and chemoresistance, however the precise molecular mechanism has not been fully delineated in ovarian cancer.  Methods: In this study, we generated STAT3 knockout (KO) ovarian cancer cell lines. Effect of STAT3 KO on cell proliferation, migration and spheroid formation was assessed in vitro and effect on in vivo tumor growth was tested using several tumor xenograft models. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134375/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA554895
Series		Accession: GSE134375	ID: 200134375

354. Molecular profiling stratifies diverse phenotypes of treatment-refractory metastatic castration-resistant prostate cancer
(Submitter supplied) The widespread and long-term use of potent therapies designed to repress androgen receptor (AR) signaling is changing the molecular and phenotypic landscapes of prostate cancer. We conducted molecular profiling of metastatic castration-resistant prostate cancer (mCRPC) patient specimens and patient-derived xenograft models and identified five distinct mCRPC phenotypes. Herein, we characterize an AR-low phenotype that has low AR expression with concomitant decreases in a subset of AR regulated genes, and an amphicrine phenotype that has both AR and neuroendocrine activity in the same cell. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 153 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126078/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA520923
Series		Accession: GSE126078	ID: 200126078

355. Single-cell Transcriptomics reveals multi-step adaptations to endocrine therapy
(Submitter supplied) Resistant tumours are thought to arise from the action of Darwinian selection on intratumoral genetic heterogeneity. However, clonal selection is incompatible with the late recurrence often characterising luminal breast cancers treated with endocrine therapy (ET), suggesting a more complex interplay between genetic and non-genetic factors. In the present study, we dissect the contributions of clonal genetic diversity and transcriptional plasticity during the early and late phases of ET at single-cell resolution. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122743/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506208
Series		Accession: GSE122743	ID: 200122743

356. Treatment of melanoma cell lines with CCG-222740
(Submitter supplied) The Ras/MEK/ERK pathway has been the primary focus of targeted therapies in melanoma, given that it is aberrantly activated in almost 80% of human cutaneous melanomas (~50% BRAFV600 mutations and ~30% NRAS mutations). While targeted therapies have yielded success in BRAFV600 mutant melanoma patients, such therapies have been ineffective in NRAS mutant melanomas in part due to their cytostatic effects and primary resistance in this patient population. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 40 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134320/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA554700
Series		Accession: GSE134320	ID: 200134320

357. A non-canonical role of YAP/TEAD is required for activation of estrogen-regulated enhancers in breast cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL21290 47 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125609/
Series		Accession: GSE125609	ID: 200125609

358. A non-canonical role of YAP/TEAD is required for activation of estrogen-regulated enhancers in breast cancer [GRO-seq]
(Submitter supplied) Estrogen and estrogen receptor alpha (ERα) signaling plays an essential role in ERα-positive breast cancer. ERα mainly occupies on distal enhancers within genome and requires the cooperation of additional co-factors to tune the enhancer activity. Through in vivo proximity-dependent labeling technique BioID, we identified YAP1 and TEAD4 protein as novel co-regulators of ERα. YAP and TEAD are nuclear effectors of the Hippo pathway regulating cell proliferation, organ size and tumorigenesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 6 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125607/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516912
Series		Accession: GSE125607	ID: 200125607

359. A non-canonical role of YAP/TEAD is required for activation of estrogen-regulated enhancers in breast cancer [RNA-seq]
(Submitter supplied) Estrogen and estrogen receptor alpha (ERα) signaling plays an essential role in ERα-positive breast cancer. ERα mainly occupies on distal enhancers within genome and requires the cooperation of additional co-factors to tune the enhancer activity. Through in vivo proximity-dependent labeling technique BioID, we identified YAP1 and TEAD4 protein as novel co-regulators of ERα. YAP and TEAD are nuclear effectors of the Hippo pathway regulating cell proliferation, organ size and tumorigenesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125606/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516911
Series		Accession: GSE125606	ID: 200125606

360. Durable Response of Enzalutamide-resistant Prostate Cancer to Supraphysiological Testosterone Is Associated with a Multifaceted Growth Suppression and Impaired DNA Damage Response Transcriptomic Program in Patient-derived Xenografts
(Submitter supplied) The study aims to determine SPT effect on the CRPC growth and molecular alterations using LuCaP PDX CRPC models.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 70 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124704/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA513162
Series		Accession: GSE124704	ID: 200124704

361. GPRC5A facilitates cell proliferation and bone metastasis of prostate cancer.
(Submitter supplied) Prostate cancer is a high frequent disease. Early stage prostate cancer can be cured with high probability by early treatment, but hormone refractory prostate cancer and progressive prostate cancer is poor prognosis. Orphan GPCRs have the potential to become a drug discovery target in various carcinomas, but there are few reports in prostate cancer and there are still many possibilities. By big data analysis, we focused on the biological properties of the prostate cancer cell line and found GPRC5A from Orphan GPCR as one of the regulators of prostate cancer development. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121319/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497056
Series		Accession: GSE121319	ID: 200121319

362. EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms 61 Samples
FTP download: GEO (BW, TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130231/
Series		Accession: GSE130231	ID: 200130231

363. EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells (RNA-Seq)
(Submitter supplied) We identified a novel cofactor of PRC2, expressed predominantly in the gonad, that limits PRC2 enzymatic activity by impeding the interaction between the core complex and the accessory subunits.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16417 GPL19057 GPL16791 33 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130229/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA534325
Series		Accession: GSE130229	ID: 200130229

364. Transcriptional responses to interferon require Mediator kinase-dependent pause release and mechanistically distinct functions of CDK8 and CDK19
(Submitter supplied) Transcriptional responses to interferon require Mediator kinase-dependent pause release and mechanistically distinct functions of CDK8 and CDK19.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129501/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA531516
Series		Accession: GSE129501	ID: 200129501

365. The effects of U1 snRNA mutation in chronic lymphocytic leukemia cell lines
(Submitter supplied) Despite an intensive search for non-coding cancer drivers, only a few have been discovered to date and none have been found among the RNAs contributing to the spliceosome. Here we report a highly recurrent A>C somatic mutation at the third base of U1 spliceosomal RNA in several tumour types. This mutation changes the preferential A-U base-pairing between U1 and 5′ splice site to C-G base-pairing, thereby creating novel splice junctions and altering the splice pattern of multiple genes, including those related to cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TAB, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134197/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA554268
Series		Accession: GSE134197	ID: 200134197

366. Systematic identification of cancer cell vulnerabilities to natural killer cell-mediated immune surveillance
(Submitter supplied) RNA-seq analysis of the transcriptome of K562 cells in which PTPN2 or DCAF15 had been disrupted by CRISPR/cas9 gene editing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 28 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134173/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA554137
Series		Accession: GSE134173	ID: 200134173

367. Colorectal cancer cells respond differentially to autophagy inhibition in vivo
(Submitter supplied) inhibition of autophagy in vivo had a substantial cell line-dependent impact on tumor growth of different CRC derived cell lines.  RNA sequencing of WT and RAB21 KD tumors in a CAM model was used to determine the gene expression profile associated with these differential responses.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134095/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA553764
Series		Accession: GSE134095	ID: 200134095

368. Genome-wide CRISPR-Cas9 screen identifies SLC1A3 as a key contributor to L-asparaginase Resistance in Solid tumors
(Submitter supplied) L-asparaginase (ASNase) has been incorporated in the treatment of acute lymphoblastic leukemia for decades. However, intolerable toxicity due to increasing ASNase dosage has been observed in clinical trials with solid tumors. Here, we performed a genome-wide CRISPR-Cas9 functional screen in ASNase-resistant PC3 prostate cancer cells and identified SLC1A3, an aspartate transporter highly expressed in brain tissues but also in several tumor types. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134074/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA553692
Series		Accession: GSE134074	ID: 200134074

369. The pause-initiation limit restricts transcription activation in human cells
(Submitter supplied) Eukaryotic gene transcription is often controlled at the level of RNA polymerase II (Pol II) pausing in the promoter-proximal region. Pausing Pol II limits the frequency of transcription initiation (‘pause-initiation limit’), predicting that the pause duration must be decreased for transcriptional activation. To test this prediction, we conducted a genome-wide kinetic analysis of the heat shock response in human cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 26 Samples
FTP download: GEO (BW, GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123980/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510428
Series		Accession: GSE123980	ID: 200123980

370. Kinome profiling of Non-Hodgkin’s lymphoma reveals Tyro3 is important in primary effusion lymphoma survival
(Submitter supplied) Non-Hodgkin’s lymphomas (NHL) make up the majority of lymphoma diagnoses and represent a very diverse set of malignancies. We sought to identify kinases uniquely upregulated in different NHL subtypes. Using Multiplexed Inhibitor Bead-mass spectrometry (MIB/MS), we found Tyro3 was uniquely upregulated and important for cell survival in primary effusion lymphoma (PEL). We developed an inhibitor against Tyro3 named UNC3810A, which inhibited cell growth in PEL but not in other NHL subtypes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 24 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114791/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472630
Series		Accession: GSE114791	ID: 200114791

371. The effect of slow and rapid H2S production on the levels of LPS-induced proinflammatory mediators and transcription in different human cell cultures
(Submitter supplied) In this study we investigated the effect of two different agents producing hydrogen sulfide (H2S) on LPS-induced inflammatory mediators such as TNFa, NO and ROS. The agents (GYY4137 and sodium hydrosulfide) applied differ significantly by the kinetics of H2S release. In the investigation we compared the effects of H2S release on the LPS-induced inflammation exploring SH-SY5Y human neuroblastoma cell line and human promonocytic cell line, THP-1. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133942/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA553180
Series		Accession: GSE133942	ID: 200133942

372. CircMYBL2 Regulates FLT3-ITD FLT3AML Translation in AML
(Submitter supplied) CircMYBL2 is more highly expressed in AML patients with FLT3-ITD mutations than in those without the FLT3-ITD mutation. We found that circMYBL2 knockdown specifically inhibits proliferation and promotes the differentiation of FLT3-ITD AML cells in vitro and in vivo. We used the ribosome profiling and RNA-seq libraries sequenced with Illumina HiSeq 2500 to identify the mRNA that circMYBL2 targeted. Interestingly, we found that circMYBL2 significantly influences the protein level of mutant FLT3 kinase, which contributes to the activation of FLT3-ITD-dependent signaling pathways. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL24676 8 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133925/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA553142
Series		Accession: GSE133925	ID: 200133925

373. Supraphysiological Androgens Repress Prostate Cancer Growth and Induce DNA Damage Augmented by PARP Inhibition
(Submitter supplied) Prostate cancer (PC) is initially dependent on androgen receptor (AR) signaling for survival and growth. Therapeutics designed to repress AR activity, such as those reducing circulating androgen levels, serve as the primary intervention for advanced disease. However, supraphysiological androgen (SPA) concentrations, can produce a paradoxical response leading to growth inhibition. We sought to determine the mechanisms by which SPA represses PC growth and determine if molecular context associates with anti-tumor effects.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119598/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489692
Series		Accession: GSE119598	ID: 200119598

374. Response of triple negative breast cancer to BAZ2A/B inhibition and BET bromodomain inhibition alone and in combination
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 48 Samples
FTP download: GEO (BED, NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116919/
Series		Accession: GSE116919	ID: 200116919

375. Response of triple negative breast cancer to BAZ2A/B inhibition and BET bromodomain inhibition alone and in combination (RNAseq)
(Submitter supplied) Three triple negative breast cancer cell lines (MDAMB231, SUM159, and HCC1806) were treated with small molecule inhibitors (JQ1, BET bromodomain inhibitor; GSK2801, BAZ2A/B bromodomain inhibitor) alone and in combination for 72 hours
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116907/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480603
Series		Accession: GSE116907	ID: 200116907

376. Race-specific  transcriptome and Long non-coding RNA  of ADT-resistant African-American prostate cancer cell models.
(Submitter supplied) Purpose: The goals of this study are to compare NGS-derived Androgen Deprivation Therapy (ADT) resistant  transcriptome  to  profiling (RNA-seq) to  Androgen Deprivation Therapy (ADT) sensitive transcriptome in African American prostate cancer cells  and validate  by reverse transcription polymerase chain reaction (qRT–PCR) methods. Method: Total RNA was extracted from different CaP cell who were ADT sensitive and  ADT resistance. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115307/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474510
Series		Accession: GSE115307	ID: 200115307

377. PAK4 suppresses RELB to prevent senescence-like growth arrest in breast cancer
(Submitter supplied) Overcoming cellular growth restriction, including the evasion of cellular senescence, is a hallmark of cancer. We report that PAK4 is overexpressed in all human breast cancer subtypes and associated with poor patient outcome. In mice, MMTV-PAK4 overexpression promotes spontaneous mammary cancer, while PAK4 gene depletion delays MMTV-PyMT driven tumors. Importantly, PAK4 prevents senescence-like growth arrest in breast cancer cells in vitro, in vivo and ex vivo, but is not needed in non-immortalized cells, while PAK4 overexpression in untransformed human mammary epithelial cells abrogates H-Ras-V12-induced senescence. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112817/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA449083
Series		Accession: GSE112817	ID: 200112817

378. A novel lncRNA lncRNA-AF339830 promotes colorectal carcinogenesis and glucose metabolism by stabilizing and specifying the transcription modification pattern of c-Myc
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL21290 GPL16791 8 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132888/
Series		Accession: GSE132888	ID: 200132888

379. Gene expression profiling of human colon cancer cell lines implanted in colon and liver of mice
(Submitter supplied) RNA was isolated from individual macrodissected tumors 4 weeks post implantation. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech's ExpressionPlot database is PRJ0019861
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 40 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125382/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516064
Series		Accession: GSE125382	ID: 200125382

380. A novel lncRNA lncRNA-AF339830 promotes colorectal carcinogenesis and glucose metabolism by stabilizing and specifying the transcription modification pattern of c-Myc [RNA-Seq]
(Submitter supplied) To elucidate whether  lncRNA-AF339830 plays a role in  colorectal cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of  lncRNA-AF339830 siRNA and control siRNA transfectants.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119866/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490516
Series		Accession: GSE119866	ID: 200119866

381. The Molecular Dissection of the Oncogenic Role of ETS1 in the Mesenchymal Subtypes of Head and Neck Squamous Cell Carcinoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 26 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109896/
Series		Accession: GSE109896	ID: 200109896

382. The Molecular Dissection of the Oncogenic Role of ETS1 in the Mesenchymal Subtypes of Head and Neck Squamous Cell Carcinoma [RNA-seq knock-down]
(Submitter supplied) RNA-Sequencing Analysis of gene expression changes due to ablation of Ets1 in SCC25 Cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109886/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432253
Series		Accession: GSE109886	ID: 200109886

383. The Molecular Dissection of the Oncogenic Role of ETS1 in the Mesenchymal Subtypes of Head and Neck Squamous Cell Carcinoma [RNA-seq Cell lines]
(Submitter supplied) RNA-Sequencing Analysis was performed on 7 Head and Neck Squamous Cell Carcinoma Cells Lines in order to examine their overall gene expression profiles.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109885/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432254
Series		Accession: GSE109885	ID: 200109885

384. single cell RNA-seq analysis of adult and paediatric IDH-wildtype Glioblastomas
(Submitter supplied) To understand the diversity of expression states in IDH-wildtype Glioblastomas, we profiled 24,131 single cells from 28 patients with GBM by single-cell RNA sequencing (7,930 cells by Smartseq2 and 16,201 by 10X).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (TSV, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131928/
Series		Accession: GSE131928	ID: 200131928

385. High-throughput RNA sequencing on circular RNA profiles of human pancreatic cancer cell lines and gemcitabine resistant pancreatic cancer cell lines.
(Submitter supplied) Gemcitabine resistance is currently the main problem of chemotherapy for advanced pancreatic cancer patients. The resistance is thought to be caused by altered drug metabolism or reduced apoptosis of cancer cells. However, the underlying mechanism of Gemcitabine resistance in pancreatic cancer remains unclear. In this study, we established Gemcitabine resistant PANC-1 (PANC-1-GR) cell lines and compared the circular RNAs (circRNAs) profiles between PANC-1 cells and PANC-1-GR cells by RNA sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110580/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434013
Series		Accession: GSE110580	ID: 200110580

386. Dtx3L and Androgen Signaling in Prostate Cancer
(Submitter supplied) Gene expression in VCaP prostate cancer cells treated with or without androgen was analyzed. VCaP cells containing a dox-inducible shRNA against Dtx3L were compared with and without dox induction (Dtx3L knockdown), in the presence or absence of androgen.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133876/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA552857
Series		Accession: GSE133876	ID: 200133876

387. LKB1-deficient and LKB1-reconstituted A549 NSCLC cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL15520 GPL18573 8 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128873/
Series		Accession: GSE128873	ID: 200128873

388. Gene responses to LKB1 overexpression in NSCLC cell line A549
(Submitter supplied) Differential gene expression analysis of LKB1-deficient and LKB1-reconstituted A549 NSCLC cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 2 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128872/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529196
Series		Accession: GSE128872	ID: 200128872

389. BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL15520 GPL18573 10 Samples
FTP download: GEO (CSV, FA) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107723/
Series		Accession: GSE107723	ID: 200107723

390. LncRNA NONHSAT113026 represses renal cell carcinoma tumorigenesis through interacting with NF-κB/p50 and SLUG
(Submitter supplied) We provide evidence that NOAT113026 inhibits renal cancer proliferative and mobility potential by blocking NF-κB/p50 and SLUG expression, which consequently inhibiting the production of oncogenic chemokines and metastasis-promoting genes. Our findings manifest that NOAT113026 may become a critical and feasible target for RCC treatment because of its anti-proliferative and anti-metastatic properties and emerge as an important biomarker for the detection of overall survival and disease-free survival.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133677/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA552219
Series		Accession: GSE133677	ID: 200133677

391. An Improved Human smORF Annotation Workflow Combining De Novo Transcriptome Assembly and Ribo-Seq
(Submitter supplied) Protein-coding small open reading frames (smORFs) are emerging as an important class of genes, however, the coding capacity of smORFs in the human genome is unclear. By integrating de novo transcriptome assembly and Ribo-Seq, we confidently annotate thousands of novel translated smORFs in three human cell lines. We find that smORF translation prediction is noisier than for annotated coding sequences, underscoring the importance of analyzing multiple experiments and footprinting conditions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 33 Samples
FTP download: GEO (GTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125218/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515538
Series		Accession: GSE125218	ID: 200125218

392. Developmental origins define epigenomic differences between subcutaneous and visceral adipocytes [RNA_seq_Whole]
(Submitter supplied) To understand the molecular differences between adipocytes and their contribution to cell-type specific function, we comprehensively characterised the transcriptomes and DNA methylomes using WGBS of isolated adipocytes from the SAT and VAT from normal weight individuals
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110915/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434804
Series		Accession: GSE110915	ID: 200110915

393. Developmental origins define epigenomic differences between subcutaneous and visceral adipocytes [RNA-Seq]
(Submitter supplied) To understand the molecular differences between adipocytes and their contribution to cell-type specific function, we comprehensively characterised the transcriptomes and DNA methylomes using WGBS of isolated adipocytes from the SAT and VAT from normal weight individuals
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110820/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434654
Series		Accession: GSE110820	ID: 200110820

394. m5C Promotes Pathogenesis of the Bladder Cancer Through Stabilizing mRNAs
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Other
Platform: GPL20795 145 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133671/
Series		Accession: GSE133671	ID: 200133671

395. Gene expression data from IMR90 control, IMR90 shRRM2 and shRRM2/shp16
(Submitter supplied) Transformed and tumorigenic cells require increased deoxyribonucleotide synthesis to fuel the genome replication that sustains their unregulated cell cycle and proliferation. Therefore, it is likely that the cell cycle and nucleotide metabolism are linked. The cell cycle inhibitor p16 is a critical tumor suppressor that is lost as an early event in many human cancers. While loss of p16 is known to play a role in deregulating the cell cycle, whether loss of p16 expression affects nucleotide metabolism is unknown.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133660/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA552100
Series		Accession: GSE133660	ID: 200133660

396. Genome wide transcriptome analysis of patient matched prostate cancer using NGS technology
(Submitter supplied) Purpose: The goal of present study is to compare transcript level changes between normal and tumor of same individual Methods: Total RNA was isolated, strand specific RNA seq was performed after Ribosomal RNA removal, global transcript profiles were generated by deep sequencing, in duplicate, using Illumina Hiseq. Initial quality check was performed using FASTQC, Alignment was performed using Hisat2 against human hg19 genome. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 60 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133626/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA552058
Series		Accession: GSE133626	ID: 200133626

397. Transcriptomics analysis of gene expression in human urothelial carcinoma of the bladder (UCB) and adjacent normal tissues.
(Submitter supplied) 36 cases of UCB and 29 adjacent normal bladder tissues (22 pairs) were derived from patients diagnosed with UCB and received radial cystectomy at Sun Yat-sen University Cancer Center (SYSUCC, Guangzhou, China). Total RNA was isolated using TRIzol® Reagent (Ambion). The RNA concentration and quality were determined with NanoDrop, Qubit and agarose gel analysis. The Dynabeads® mRNA Purification Kit (Ambion) was used to enrich the mRNAs, which were used as templates for RNA-Seq library construction. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 65 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133624/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA552055
Series		Accession: GSE133624	ID: 200133624

398. Axitinib exposure triggers endothelial cells senescence through ROS accumulation and ATM activation
(Submitter supplied) Here we report that Axitinib, an inhibitor of VEGFRs currently in use as a second line treatment for advanced renal cell carcinoma, promotes senescence of human endothelial cells in vitro. Mechanistically, this requires oxidative stress-dependent activation of the Ataxia Telangiectasia Mutated (ATM) kinase. Induction of oxidative stress-related genes  distinguishes the response of endothelial cells to Axitinib from that to doxorubicin
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126426/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA521866
Series		Accession: GSE126426	ID: 200126426

399. On-Treatment Biomarkers Improve Prediction of Response to Neoadjuvant Chemotherapy in Breast Cancer
(Submitter supplied) Background: Neoadjuvant chemotherapy is increasingly being used to preoperatively shrink breast tumours prior to surgery. This approach also provides the opportunity to study the molecular changes associated with treatment and evaluate whether on-treatment sequential samples can improve response and outcome predictions over diagnostic or excision samples alone. Methods: A total of 95 samples from a cohort of 50 neoadjuvant chemotherapy-treated primary breast cancer patients (aged 29-76, 48% ER+, 20% HER2+) enrolled in the NEO trial taken before, at 2 weeks on-treatment, mid-therapy and at resection were sequenced with Ion Ampliseq transcriptome yielding expression values for 12,635 genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 95 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122630/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA505812
Series		Accession: GSE122630	ID: 200122630

400. RNA-sequencing analysis of differentially expressed genes (DEGs) induced by STC2 overexpression in colorectal cancer cells
(Submitter supplied) To identify STC2-regulated downstream target genes, we compared the results of RNA-seq analysis between colorectal cancer cells without STC2 (SW480-NC) and cells with STC2 (SW480-STC2).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116521/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA478926
Series		Accession: GSE116521	ID: 200116521

401. Arginine methylation controls cell proliferation by integrating E2F activity with the splicing machinery
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18573 17 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111961/
Series		Accession: GSE111961	ID: 200111961

402. Arginine methylation controls cell proliferation by integrating E2F activity with the splicing machinery (RNA-seq data set)
(Submitter supplied) Residue-specific arginine methylation (meR) on the E2F1 subunit plays an essential role in determining whether cell cycle progression or apoptosis ensues, although the molecular pathways underpinning the effects of methylation remain obscure.  We report here that the methylation events on E2F1 have a direct impact on the mechanisms which underpin gene expression control. Specifically, the PRMT5-mediated symR mark not only influences the transcription repertoire of genes targeted by E2F1, but also endows E2F1 with the ability to regulate RNA splicing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111960/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438683
Series		Accession: GSE111960	ID: 200111960

403. Ectopic CTCFL/BORIS expression in ovarian cancer precursor cells enhances cellular motility and invasion through GALNT14 and alters CTCF chromatin occupancy
(Submitter supplied) High-grade serous carcinoma (HGSC) is the most aggressive and predominant form of epithelial ovarian cancer and the leading cause of gynecological cancer death. We have previously shown that CTCFL (also known as BORIS, Brother of the Regulator of Imprinted Sites) is expressed in a large proportion of ovarian cancers, which is associated with global and promoter-specific DNA hypomethylation, advanced tumor stage, and poor prognosis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BED, WIG, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131931/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA545335
Series		Accession: GSE131931	ID: 200131931

404. ARID1A and PI3-Kinase pathway mutations in the endometrium drive epithelial transdifferentiation and collective invasion [12Z_RNA-seq]
(Submitter supplied) ARID1A and PI3-Kinase (PI3K) pathway alterations are common in neoplasms originating from the uterine endometrium. Here we show that monoallelic loss of ARID1A in the mouse endometrial epithelium is sufficient for vaginal bleeding when combined with PI3K activation. Sorted mutant epithelial cells display gene expression and promoter chromatin signatures associated with epithelial-to-mesenchymal transition (EMT). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (CSV, TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129782/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA532771
Series		Accession: GSE129782	ID: 200129782

405. ARID1A and PI3-Kinase pathway mutations in the endometrium drive epithelial transdifferentiation and collective invasion [12Z_1A_PI3K_RNA-seq]
(Submitter supplied) ARID1A and PI3-Kinase (PI3K) pathway alterations are common in neoplasms originating from the uterine endometrium. Here we show that monoallelic loss of ARID1A in the mouse endometrial epithelium is sufficient for vaginal bleeding when combined with PI3K activation. Sorted mutant epithelial cells display gene expression and promoter chromatin signatures associated with epithelial-to-mesenchymal transition (EMT). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (CSV, TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129779/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA532768
Series		Accession: GSE129779	ID: 200129779

406. MYC deregulates TET1 and TET2 expression to control global DNA (hydroxy)methylation and gene expression to maintain a neoplastic phenotype in T-ALL
(Submitter supplied) We performed methylation, hydroxymethylation, and gene expression profiling using MeDIP-seq, hMeDIP-seq, and RNA-seq, respectively, to investigate the role of TET1 and TET2 in MYC-driven tumor maintenance. We compared T-ALL tumor cells before and upon MYC inactivation and revealed genome-wide changes in the DNA methylation and hydroxymethylation patterns. Furthermore, TET1 knock-down or ectopic TET2 expression in T-ALL revealed genome-wide changes in DNA methylation and hydroxymethylation patterns corresponding to changes in gene expression.
Organism:	Mus musculus; Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL21103 GPL20301 18 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126029/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA520933
Series		Accession: GSE126029	ID: 200126029

407. Targeting HuH7 cells with JumonjiC Lysine Demethylase Inhibitors (RNA-Seq)
(Submitter supplied) Characterization of gene expression changes in HuH7 HCC cells upon treatment with the Jumonji KDM inhibitor, JIB-04, GSK-J4 and SD-70.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125518/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516661
Series		Accession: GSE125518	ID: 200125518

408. TMED9-gated CNIH4 and TGFa signaling promotes pro-metastatic states in human primary colon cancer cells
(Submitter supplied) How cells in primary tumors initially become pro-metastatic is not understood. A previous genome-wide RNAi screen uncovered colon cancer metastatic suppressor and WNT promoting functions of TMED3, a member of the p24 ER-to-Golgi protein secretion family. Repression of WNT signaling upon knock-down (kd) of TMED3 might thus be sufficient to drive metastases. However, searching for transcriptional influences on other family members here we find that TMED3 kd leads to enhanced TMED9, that TMED9 acts downstream of TMED3 and that TMED9 kd compromises metastasis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125282/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515737
Series		Accession: GSE125282	ID: 200125282

409. Human Lung Carcinoids
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by genome tiling array
Platforms: GPL11154 GPL13534 48 Samples
FTP download: GEO (IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118133/
Series		Accession: GSE118133	ID: 200118133

410. Transcriptomic profiling of human Lung Carcinoids (LCs)
(Submitter supplied) Lung carcinoids (LCs) are rare and slow growing primary lung neoplasms that are understudied. Here, we performed targeted exome sequencing using a 354-cancer gene panel (n=29), mRNA sequencing (n=30) and DNA methylation assay (n=18) on macro-dissected lung carcinoids. The mutations we identified were enriched for genes involved in covalent histone modification/chromatin remodeling (34.5%) (MEN1, ARID1A, KMT2C and KMT2A were recurrently mutated) as well as DNA repair (17.2%) pathways. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118131/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA484631
Series		Accession: GSE118131	ID: 200118131

411. Low cytosolic folate cycling is a hallmark of U251 glioblastoma cells reprogramming towards pluripotency
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Methylation profiling by genome tiling array; Expression profiling by high throughput sequencing
Platforms: GPL15433 GPL13534 12 Samples
FTP download: GEO (IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117544/
Series		Accession: GSE117544	ID: 200117544

412. Low cytosolic folate cycling is a hallmark of U251 glioblastoma cells reprogramming towards pluripotency [RNA-seq]
(Submitter supplied) we report that U251 glioblastoma tumor spheres exhibit low cytosolic folate cycle and a reprogrammmed mitochondrial folate cycle that is presumably oriented towards oxidizing the formyl group to CO2 with the production of TetraHydroFolate and release of NADPH instead of synthesizing formate
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117543/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482432
Series		Accession: GSE117543	ID: 200117543

413. 3D genome landscape of Epstein-Barr Virus oncoproteins and virus activated NF-kB in lymphoblastoid cells
(Submitter supplied) Epstein-Barr Virus (EBV) encoded Nuclear Antigens (EBNAs) and virus activated NF-B subunits mostly bind to enhancers in EBV transformed lymphoblastoid cells lines (LCLs). Using LCL 3D genome organization map that links EBV enhancers to promoters, we built the most comprehensive virus regulome. EBV regulome contained 1992 genes and enhancers directly linked to them. ~30% of genes essential for LCL growth were linked to EBV enhancers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 3 Samples
FTP download: GEO (FPKM_TRACKING, GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101666/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395150
Series		Accession: GSE101666	ID: 200101666

414. Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma
(Submitter supplied) Resistance to proteasome inhibitors (PIs) is a ubiquitous clinical concern in multiple myeloma (MM).  We proposed that signaling-level responses after PI would reveal new means to enhance efficacy.  Unbiased phosphoproteomics after the PI carfilzomib surprisingly demonstrated the most prominent phosphorylation changes on spliceosome components.  Spliceosome modulation was invisible to RNA or protein abundance alone. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL11154 GPL20301 43 Samples
FTP download: GEO (CSV, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124510/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512268
Series		Accession: GSE124510	ID: 200124510

415. Predicting Postoperative Liver Dysfunction Based on Blood Derived MicroRNA Signatures
(Submitter supplied) Treatment options and reliable predictive marker to determine patients at risk to develop postoperative LD and to define the optimal time point of liver resection are limited. Accordingly, there is an urgent need for an easily assessable preoperative test to predict postoperative liver function recovery, specifically as current markers are often expensive, time consuming and sometimes invasive. Emerging evidence suggests that microRNA (miRNA) signatures represent potent diagnostic, prognostic and treatment response biomarkers for several diseases. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 48 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123605/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509364
Series		Accession: GSE123605	ID: 200123605

416. MYCN knock-down leads to DNA-repair deficiency in human neuroblastoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL20795 GPL11154 GPL16791 36 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120859/
Series		Accession: GSE120859	ID: 200120859

417. MYCN knock-down leads to DNA-repair deficiency in human neuroblastoma (RNA-Seq)
(Submitter supplied) We knock down MYCN in human neuroblastoma cell line by RNAi. MYCN knock-down caused global epigenome change, including nucleosome gain on key DNA-repair genes and promoter H3K9ac down regulation.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120858/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494722
Series		Accession: GSE120858	ID: 200120858

418. RNA-Seq of Breast and Ovarian Cancer Cell Lines
(Submitter supplied) A panel of 20 commonly used cell lines were used for RNA-Seq in order to measure gene expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114332/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA470980
Series		Accession: GSE114332	ID: 200114332

419. UPF1/SMG7-dependent MicroRNA-mediated Gene Regulation
(Submitter supplied) A majority of metazoan mRNAs are under microRNA (miRNA)/Argonaute (Ago)-mediated control of RNA stability at the post-transcriptional level. Although the molecular mechanism of the miRNA-mediated repression of target mRNAs through Ago/TNRC6 pathway have been largely elucidated, however, the existence of alternative TNRC6-independent miRNA-mediated post-transcriptional gene regulation pathway remains unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99169/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387461
Series		Accession: GSE99169	ID: 200099169

420. Radiomic and gEnomic approaches for the enhanced DIagnosis of REnal Cancer (REDIRECt): A translational pilot study
(Submitter supplied) Introduction: The aim of this pilot study is to establish a radiogenomic characterisation of a clear-cell renal cell carcinoma (ccRCC) subpopulation, focusing on the transcriptomic underpinnings of radiomic features. Materials & Methods: To establish the viability of conducting a combined analysis of both radiomic and genomic data, a pilot cohort of 6 patients with <5cm G2 unilateral non-metastatic T1a-b ccRCC, who underwent surgery, was evaluated. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133460/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA551492
Series		Accession: GSE133460	ID: 200133460

421. shRNA-mediated knockdown of ETV4 and MED25 in the prostate cell line PC3 reveals set of genes potentially coregulated by MED25 and ETV4
(Submitter supplied) Our in vitro binding studies support a model whereby MED25 exhibits multivalent interactions with a subset of related ETS factors, ETV1/4/5. We hypothesize that the interaction would allow for coregulation of genes by ETV1/4/5 and MED25, acting perhaps to link the ETVs to the Mediator complex. To explore this possibility, we compared the genome occupancy for FLAG-tagged MED25 and ETV4 in the prostate cancer cell line PC3, which overexpresses ETV4. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133447/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA551469
Series		Accession: GSE133447	ID: 200133447

422. Effect of the twelve isoforms of Hepatocyte nuclear factor 4 alpha on HCT116 cell line transcriptome
(Submitter supplied) The nuclear receptor HNF4alpha is regulating a wide set of genes associated with development, cell differentiation, inflammation and metabolism. In human, 12 variants of HNF4α  can be expressed by the use of two promoters and by alternative splicing. Until now, the characterization of this transcription factor has ignored this diversity and has remained confined to the study of a fraction of the isoforms. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 39 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125852/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA517705
Series		Accession: GSE125852	ID: 200125852

423. Transcriptome characterization of radiation-induced sarcomas
(Submitter supplied) We performed RNA sequencing on secondary sarcomas, arising from previous radiation therapies. We investigated whether such radiation-induced tumours harbour specific genomic and/or transcriptomic alterations compared to sporadic (primary) sarcomas.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 77 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102055/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA396157
Series		Accession: GSE102055	ID: 200102055

424. Digital gene expression (DGE) based transcript profiling of CDK inhibitors
(Submitter supplied) We compare differences in gene expression induced after 6 hours of exposure to one of three CDK4/6 inhibitors or a pan-CDK inhibitor
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21697 335 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125215/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515531
Series		Accession: GSE125215	ID: 200125215

425. RNAseq based trascript profilling of MCF7-xenograft mice treated with one of three CDK4/6 inhibitiors
(Submitter supplied) We compare differences in gene expression induced after treating MCF7-xenograft mice with either ribociclib, palbociclib, or abemacicilb daily for 4 days.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL19415 64 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124854/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA514039
Series		Accession: GSE124854	ID: 200124854

426. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL20795 GPL11154 152 Samples
FTP download: GEO (BED, BW, NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120110/
Series		Accession: GSE120110	ID: 200120110

427. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [GRO-Seq]
(Submitter supplied) Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA binding proteins (RBPs). Although multiple RBPs have been implicated in transcriptional control, it has remained unclear how extensively RBPs directly act on chromatin. We embarked on a large-scale RBP ChIP-seq analysis, revealing widespread RBP presence in active chromatin regions in the human genome. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 38 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120105/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA491665
Series		Accession: GSE120105	ID: 200120105

428. Multiomics Profiling Establishes the Polypharmacology of FDA-Approved CDK4/6 Inhibitors and the Potential for Differential Clinical Activity.
(Submitter supplied) We compared three CDK4/6 inhibitors that have recently emerged as highly promising agents for advanced breast cancers by performing transcriptional profiling (mRNA-Seq) on a panel of seven breast cancer cell lines following 6 or 24 hours of drug exposure at concentrations ranging from 0.3 to 3.0 uM.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 120 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99116/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387311
Series		Accession: GSE99116	ID: 200099116

429. Transcriptome studies of marine natural products 4a and 4d on non-small cell lung cancer A549 cells
(Submitter supplied) Two novel polyketides, ocellatusones A and B (1 and 2), characterized by either an uncommon oxatricyclo[4.2.1.02,4]nonane skeleton (1) or a mesitylene connected dimethylfuran-3(2H)-one nucleus (2), were isolated in racemic forms from the South China Sea sacoglossan Placobranchus ocellatus, together with seven uncommon polypropionates (3, 4a,4d, 5, and 6). Compounds 1 and 2 were further separated by chiral HPLC to their corresponding enantiomers (±)-1 and (±)-2, respectively. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132500/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA548185
Series		Accession: GSE132500	ID: 200132500

430. Integrative transcriptomic analysis reveals mechanisms controlling the reciprocity of epithelial and mesenchymal genes during epithelial-to-mesenchymal transition
(Submitter supplied) Epithelial-to-mesenchymal transition (EMT) is an important developmental process that is also activated during disease progressions. Many genes involved in EMT have been identified to date, but the key molecules governing the coupling between the dynamics of epithelial genes and that of the mesenchymal genes are unclear. In addition, it has been shown that there is a remarkable diversity of EMT phenotypes in different pathological conditions or microenvironments, but its mechanistic basis remains elusive. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124843/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA513977
Series		Accession: GSE124843	ID: 200124843

431. KMT9a writes the H4K12me1 histone mark and controls metabolism and proliferation of castration-resistant prostate cancer cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.  Posttranslational modifications of histones such as methylation regulate chromatin structure and gene expression. Methylation of histone lysine residues is generally performed by SET domain methyltransferases. Here, we identify the heterodimeric C21orf127/TRMT112 complex as a histone methyltransferase. Assembly of the seven-b-strand protein C21orf127 (also named Hemk2, N6amt1 or PrmC) with TRMT112 is essential to form an active enzyme, hereafter named KMT9 that writes the histone mark H4K12me1 in vitro and in vivo. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 34 Samples
FTP download: GEO (BED, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117536/
Series		Accession: GSE117536	ID: 200117536

432. KMT9a writes the H4K12me1 histone mark and controls metabolism and proliferation of castration-resistant prostate cancer cells [RNA-seq]
(Submitter supplied) The aim of the RNA-seq was to identify the KMT9 transcriptome in PC-3M cells. The MCF10A breast epithelial cells that do not express KMT9a were used to show that the siRNA against KMT9 show no off-target effects.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117535/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482410
Series		Accession: GSE117535	ID: 200117535

433. ERα-CtBP-mediated repression of Homologous-recombination repair in ovarian cancer improves chemo-sensitivity
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116018/
Series		Accession: GSE116018	ID: 200116018

434. ERα-CtBP-mediated repression of Homologous-recombination repair in ovarian cancer improves chemo-sensitivity [ChIP-seq]
(Submitter supplied) Deficiency in homologous recombination repair (HRR) is frequently associated with hormone-responsive cancers. Epithelial ovarian cancer (EOC) is a typical hormone-related tumor, with defects of HRR in up to half of cases. However, whether there are molecular connections between estrogen signaling and HRR deficiency in EOC remains unknown. Here we report an inverse correlation between estrogen signaling and HRR activity in EOC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (BW, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116005/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476785
Series		Accession: GSE116005	ID: 200116005

435. ERα-CtBP-mediated repression of Homologous-recombination repair in ovarian cancer improves chemo-sensitivity [RNA-seq]
(Submitter supplied) Deficiency in homologous recombination repair (HRR) is frequently associated with hormone-responsive cancers. Epithelial ovarian cancer (EOC) is a typical hormone-related tumor, with defects of HRR in up to half of cases. However, whether there are molecular connections between estrogen signaling and HRR deficiency in EOC remains unknown. Here we report an inverse correlation between estrogen signaling and HRR activity in EOC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 5 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115481/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475140
Series		Accession: GSE115481	ID: 200115481

436. Stromal Mir-20a modulates paracrine CXCL8 secretion in colitis and colon cancer
(Submitter supplied) We report the results of RNA-Seq on fibroblasts cultivated from cancerous, colitic and normal primary patient colon tissues
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106119/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA415631
Series		Accession: GSE106119	ID: 200106119

437. Epithelial-mesenchymal transition markers screenedina cell-based model and validated in lung adenocarcinoma
(Submitter supplied) The epithelial-to-mesenchymal transition (EMT) process in cancer enables the migratory and invasive capabilities associated with metastatic competence. The cancer microenvironment plays an important role in inducing the occurrence of EMT. A number of extracellular stimuli and associated signaling pathways have been identified to promote EMT, however, molecular features during the early stages of EMT are poorly understood. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL18573 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90133/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354518
Series		Accession: GSE90133	ID: 200090133

438. RNA-seq of human normal lung and lung cancer tissue
(Submitter supplied) In order to identify divergent transcripts involved in cancer development, next-generation sequencing analysis of RNA extracted from cancer and normal lung tissue was performed.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133206/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA550383
Series		Accession: GSE133206	ID: 200133206

439. High-throughput sequence analysis of peripheral T-cell lymphomas indicates subtype specific viral gene expression patterns and immune cell microenvironments
(Submitter supplied) Certain peripheral T-cell lymphomas (PTCLs) have been associated with viral infection, particularly infection with Epstein-Barr virus (EBV). However, a comprehensive virome analysis across PTCLs has not previously been reported, and viral gene expression profiles have been studied only in certain PTCL subtypes. In this study we utilized published RNA-seq data sets from seven different PTCL studies as well as new RNA-seq data from our laboratory to screen for virus association, to analyze viral gene expression, and to assess B- and T-cell receptor diversity paradigms across these tumor types. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131261/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA543084
Series		Accession: GSE131261	ID: 200131261

440. Disparate anticancer activity of structurally similar multi-kinase inhibitors through cumulative differential effects on individual targets
(Submitter supplied) Despite recent improvements many cancer patients do not respond to immune or targeted drugs and require new therapies. Through a systems pharmacology approach including phenotypic screening, chemical and phosphoproteomics and RNA-Seq, we elucidated the mechanism of action underlying the differential anticancer activity of two structurally related multi-kinase inhibitors, foretinib and cabozantinib, in lung cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126850/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA523517
Series		Accession: GSE126850	ID: 200126850

441. Single-cell profiling of cutaneous T-cell lymphoma after treatment with vorinostat and photophoresis.
(Submitter supplied) Cutaneous T cell lymphomas (CTCL), encompassing a spectrum of T-cell lymphoproliferative disorders involving the skin, have collectively increased in incidence over the last 40 years. Sézary syndrome (SS) is an aggressive form of CTCL characterized by significant presence of malignant cells in both the blood and skin. The guarded prognosis for SS reflects a lack of reliably effective therapy, due in part to an incomplete understanding of disease pathogenesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124898/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA514236
Series		Accession: GSE124898	ID: 200124898

442. RNA sequencing data of human prostate cancer cells treated with androgen
(Submitter supplied) To analyse and understand the differentially expressed genes following treatment with synthetic androgen (R1881)
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 11 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128749/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA528760
Series		Accession: GSE128749	ID: 200128749

443. RNA-sequencing analysis for gene expression profiles affected by CASC9 knockdown
(Submitter supplied) Genome-wide association studies of tumor samples have identified a large number of lncRNAs associated with various types of cancer including colorectal cancer. To elucidate the mechanism by which CASC9 regulates colorectal cancer cell growth, RNA-sequencing was performed to analyze the gene expression profile affected by CASC9 knockdown. A total of 249 significantly upregulated genes and 491 significantly downregulated genes (absolute fold change ≥ 2, P < 0.05) were found in CASC9 knockdown HCT-116 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125648/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA517086
Series		Accession: GSE125648	ID: 200125648

444. Functional diversity of inhibitors tackling the differentiation arrest of MLL-rearranged leukemia
(Submitter supplied) Purpose: The chromosomal rearrangements of the mixed-lineage leukemia (MLL) gene have been extensively characterized as a potent oncogenic driver on the molecular and mechanistic level in acute lymphoblastic (ALL) and acute myeloid (AML) leukemia. For its oncogenic function the MLL fusion protein is hijacking the the multi enzyme super elongation complex (SEC) leading to elevated expression of MLL target genes (e.g. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 305 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125437/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516400
Series		Accession: GSE125437	ID: 200125437

445. Selective Targeting of PARP2 Inhibits Androgen Receptor Signaling and Prostate Cancer Growth Through Disruption of FOXA1 Function
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 31 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114275/
Series		Accession: GSE114275	ID: 200114275

446. Gene expression profilings for prostate cancer cells after inhibition of PARP1 or PARP2 using pharmaceutical or siRNA-based approaches
(Submitter supplied) Androgen receptor (AR) signaling is a key driver of prostate cancer (PCa) growth and progression. Understanding the factors influencing AR-mediated transcription provides new opportunities for therapeutic intervention. We have previously discovered that a genetic variant in one of the DNA repair genes, PARP2, is associated with aggressive PCa. Here, we show that a high expression level of PARP2 in PCa tumors is associated with high Gleason scores and biochemical recurrence using The Cancer Genome Atlas (TCGA) dataset. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114273/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471001
Series		Accession: GSE114273	ID: 200114273

447. Convergence of BMI1 and CHD7 on ERK signalling in medulloblastoma
(Submitter supplied) We describe a novel molecular convergence between BMI1 and CHD7 in the initiation of medulloblastoma. We show that CHD7 controls differentiation of G4 MB cells and its silencing renders them susceptible to Bmi1-mediated ERK1/2-induced proliferation control. We show that BMI1-mediated repression of the ERK1/2 inhibitor DUSP4 leads to increased proliferation and tumour burden in primary human MB cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83696/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326747
Series		Accession: GSE83696	ID: 200083696

448. IBL-302 PIM/PI3K/mTOR triple kinase inhibitor treatment of patient derived orthotopic xenograft neuroblastoma cells
(Submitter supplied) neuroblastoma cells derived from PDOX models were treated with the kinase inhibitor.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24014 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133137/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA550081
Series		Accession: GSE133137	ID: 200133137

449. Transcriptomic analysis of 5637 bladder cancer cell line transfected with MAT1A plamid, 48 hours post transfection
(Submitter supplied) Transcriptomic analysis of 5637 bladder cancer cell line transfected with MAT1A plamid, 48 hours post transfection
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133123/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA550034
Series		Accession: GSE133123	ID: 200133123

450. Chemotherapeutic drugs inhibiting Topoisomerase 1 activity inhibit TNF-induced inflammatory gene expression
(Submitter supplied) Inhibitors of DNA topoisomerase I (TOP1), an enzyme relieving torsional stress of DNA by generating transient single-strand breaks, are clinically used to treat ovarian cancer, small cell lung cancer and cervical cancer. As torsional stress is generated by replication and transcription we tested the effects of clinically used TOP1 inhibitors Topotecan and SN-38 on TNF-induced gene expression. RNA-seq experiments showed that inhibition of TOP1 activity interfered with the vast majority of TNF-triggered genes, while interference with TOP2 activity had only a minor impact. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128798/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA528902
Series		Accession: GSE128798	ID: 200128798

451. Single Cell mRNA Sequencing of Pca-associated CD14+CD11b+ macrophages
(Submitter supplied) Purpose: Androgen receptor (AR) is a crucial modulator of prostate cancer (PCa) cells behaviour, and AR expression has been found in several stromal cells, including macrophages, however its role in these cells in largely unknown. In this study, we described the molecular mechanims and the functional implications of AR activation and blockade in macrophages in relation to PCa progression. Results: Analysis showed the transcriptomic landscape of PCa-associated macrophages Conclusions: Our study represents the first detailed analysis of AR molecular function in Pca-associated macrophages
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 3 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133094/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA549935
Series		Accession: GSE133094	ID: 200133094

452. Alu RNA modulates the expression of cell cycle genes in human fibroblasts
(Submitter supplied) Alu retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate Alu RNAs, represent the most numerous non-coding RNA (ncRNA) gene family in the human genome. Alu transcription is generally kept to extremely low levels by tight epigenetic silencing, but it has been reported to increase under different types of cell perturbation, such as viral infection and cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133078/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA549888
Series		Accession: GSE133078	ID: 200133078

453. Expression data from ME180 cells transfected with siControl and siSGK1
(Submitter supplied) SGK1 knockdown-induced transcriptional changes in ME180 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130449/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540275
Series		Accession: GSE130449	ID: 200130449

454. Analyses of a panel of transcripts and construction of RNA networks in hepatocellular carcinoma
(Submitter supplied) To identify HCC-related RNAs, we used four HCC patients’ fresh tumor tissues and paired adjacent non-tumor tissues for RNA sequencing. Differential expression of mRNAs, lncRNAs, circRNAs and miRNAs were then analyzed
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL18573 16 Samples
FTP download: GEO (FA) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128274/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA526922
Series		Accession: GSE128274	ID: 200128274

455. Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis
(Submitter supplied) A comprehensive understanding of the changes in gene expression in cell  types involved in idiopathic pulmonary fibrosis (IPF) will shed light on the  mechanisms underlying the loss of alveolar epithelial cells, and  development of honeycomb cysts and fibroblastic foci. We sought to  understand changes in IPF lung cell transcriptomes and gain insight into  innate immune aspects of pathogenesis. We investigated IPF  pathogenesis using single cell RNA-sequencing of fresh lung explants,  comparing human IPF fibrotic lower lobes reflecting late disease, upper  lobes reflecting early disease and normal lungs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128033/
Series		Accession: GSE128033	ID: 200128033

456. TGF-β promotes genomic instability after loss of RUNX3
(Submitter supplied) Studies of genomic instability have historically focused on intrinsic mechanisms rather than extrinsic  mechanisms based in the tumor microenvironment (TME). TGF-β is the most abundantly secreted  cytokine in the TME where it imparts various aggressive characteristics including invasive migration,  drug resistance and epithelial-to-mesenchymal transition (EMT). Here we show that TGF-β also  promotes genomic instability in the form of DNA double strand breaks (DSB) in cancer cells which  lack the tumor suppressor gene RUNX3. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133037/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA549732
Series		Accession: GSE133037	ID: 200133037

457. RNA sequence of mRNA in HUVEC cells after depleting EGFL6
(Submitter supplied) Total RNA was isolated from each thymic sample using the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA). RNA quality was examined by gel electrophoresis and with a Nanodrop spectrophotometer (Thermo, Waltham, MA, USA). For RNA sequencing, RNA samples from 9 biological replicates were separated into three independent pools, each comprised of three distinct samples at equal amounts. Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), and sequencing was carried out using the Illumina HiSeq X Ten instrument by the commercial service of Genergy Biotechnology Co. Ltd. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133000/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA549677
Series		Accession: GSE133000	ID: 200133000

458. USP8 mutations determine genes’ expression profile of pituitary corticotroph adenomas, regardless of tumor functional status.
(Submitter supplied) The aim of the study was to compare genes’ expression profiles of functioning and silent corticotroph adenomas to investigate possible biological mechanism of different hormone secretion . Since USP8 is the best know driver gene mutated in large proportion of ACTH-omas we intended to verify whether the mutation occurs in SCAs and how it affects transcriptomic profile.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 20 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132982/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA549652
Series		Accession: GSE132982	ID: 200132982

459. Gene expression analysis of ER+ and ER- breast cancer cell lines with acquired resistance to palbociclib
(Submitter supplied) While targeted therapies directed against cancer cells have proven effective, their clinical benefit is often limited by acquired resistance. This clinical challenge underscores the importance of uncovering the molecular mechanisms behind resistance in order to develop novel targets and drug combinations that can stop the growth of cancer cells. Two pivotal pathways controlling tumor growth are glucose metabolism and cell cycle. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130437/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540259
Series		Accession: GSE130437	ID: 200130437

460. Transcriptome Analysis Reveals Distinct Responses to Physiologic versus Toxic Manganese Exposure in Human Neuroblastoma Cells
(Submitter supplied) We report the application of RNA-Seq analysis to determine the transcriptional responses to Mn dose, ranging from physiological to toxicological levels in human SH-SY5Y neuroblastoma cells. We find that Mn dose showed widespread effects in abundance of protein coding genes for metabolism of reactive oxygen species, energy sensing, glycolysis, protein homeostasis including the unfolded protein response and transcriptional regulation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129336/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA530967
Series		Accession: GSE129336	ID: 200129336

461. Expression data from A2780 cells treated with DMSO, Olaparib(Ola), Palbociclib(PD), and their combination (Ola/PD)
(Submitter supplied) Drug treatment-induced transcriptional changes in A2780 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126998/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA524121
Series		Accession: GSE126998	ID: 200126998

462. HOXC10 Overexpression Promotes Cell Proliferation and Migration through Regulation of CST1 Expression in Gastric Cancer
(Submitter supplied) This study propose HOXC10 overexpression by reduced DNA methylation promotes gastric cancer progression through regulation of CST1 and S100P.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119196/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488452
Series		Accession: GSE119196	ID: 200119196

463. Human pluripotent stem cell-derived brain tumor model uncovered embryonic stem cell signature as a key driver in atypical teratoid/rhabdoid tumor (RNA-Seq)
(Submitter supplied) Atypical teratoid/rhabdoid tumor (AT/RT), which harbors INI1 mutation and exhibits a characteristic histology of rhabdoid cells, has a poor prognosis because of the lack of effective treatments. Here we established human INI1-deficient pluripotent stem cells (hPSCs), which developed AT/RT formation in vivo. We revealed that the activation of ESC-like signature leads to rhabdoid phenotype in tumor by OSKM or c-MYC induction. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118654/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486353
Series		Accession: GSE118654	ID: 200118654

464. Potent anti-tumor efficacy of palbociclib in H3K27M-mutant diffuse intrinsic pontine glioma
(Submitter supplied) Diffuse intrinsic pontine glioma (DIPG) is a rare and fatal pediatric brain cancer without cure. DIPG has high percentage histone mutation at K27M on histone H3 locus, which is believed to be one of the drivers of the tumorigenesis. Dysregulation of G1/S cell cycle checkpoint is more enriched in the H3.3K27M mutant subgroup. In this study, we reported that palbociclib (PD0332991), a specific and cytostatic inhibitor of CDK4/6, effectively suppresses the growth of DIPG cells in vitro and in vivo. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 4 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115976/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476614
Series		Accession: GSE115976	ID: 200115976

465. Transcriptomics changes in liver metastatic biopsies of colorectal carcinoma between pre-treated and acquired resistance to Cetuximab
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84270/
Series		Accession: GSE84270	ID: 200084270

466. Transcriptomics changes in liver metastatic biopsies of colorectal carcinoma between pre-treated and acquired resistance to Cetuximab [mRNA]
(Submitter supplied) Two patients who were newly diagnosed and pathologically confirmed metastatic colorectal cancer were screened for eligibility between August 2011 and December 2013 in Affiliated Hospital, Academy of Military Medical Sciences. They were treated with Cetuximab in combination with FOLFOX regimen and obtained continuous partial responses in more than six months. CT scans of liver lesions were performed every two to eight weeks. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84267/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328500
Series		Accession: GSE84267	ID: 200084267

467. Transcriptome Analysis and Functional Identification of Adipose-Derived Mesenchymal Stem Cells in Secondary Lymphedema
(Submitter supplied) We isolated adipose-derived mesenchymal stem cells (ASCs) from the lymphedema adipose tissue from liposuction specimens of 10 patients with malignancy-related extremity lymphedema, and we used adipose tissue from the normal upper abdomen of the same patients as control tissue. We compared the proliferation and adipogenic differentiation capacity between the two kinds of ASCs, and we explored the transcriptomic differences between them. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 20 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132936/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA549491
Series		Accession: GSE132936	ID: 200132936

468. Spliceosomal disruption of the non-canonical BAF complex in cancer
(Submitter supplied) SF3B1 is the most commonly mutated RNA splicing factor in cancer, but the mechanisms by which SF3B1 mutations promote malignancy are poorly understood. Here, we integrated pan-cancer RNA sequencing to identify mutant SF3B1-dependent aberrant splicing with a positive enrichment CRISPR screen to prioritize splicing alterations that functionally promote tumorigenesis. We identify that diverse, recurrent SF3B1 mutations converge on repression of BRD9, a core component of the recently described non-canonical BAF (ncBAF) complex. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL18573 21 Samples
FTP download: GEO (BW, NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124720/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA513262
Series		Accession: GSE124720	ID: 200124720

469. Whole transcriptome sequencing of the human thyroid primary cells with knock-down of the NRG1 gene
(Submitter supplied) The protein encoded by the NRG1 gene is a membrane glycoprotein that mediates cell-cell signaling and plays a critical role in the growth and development of multiple organ systems. Here we report gene expression profiles of human thyroid primary cells on Day 5 treated with NRG1 siRNA. The primary cells were generated from fresh nontumorous thyroid tissues obtained from thyroid cancer patients. A number of new dysregulated genes of NRG1 were discovered. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100322/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391313
Series		Accession: GSE100322	ID: 200100322

470. Overexpression of eukaryotic translation initiation factor, eIF4E confers tamoxifen resistance in breast cancer via the ERα/FOXM1 axis
(Submitter supplied) We report the application of RNA sequencing technology for high-throughput profiling of mRNA expression in breast cancer cell line
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132851/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA549272
Series		Accession: GSE132851	ID: 200132851

471. Next Generation RNA Sequencing of Glioblastoma Cancer Associated Fibrobasts
(Submitter supplied) Cancer Fibroblasts Isolated from 2 GBM Cases.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132825/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA549185
Series		Accession: GSE132825	ID: 200132825

472. A Human Liver Cell Atlas reveals Heterogeneity and Epithelial Progenitors 
(Submitter supplied) We perfomed single-cell RNA-sequnecing of around 10,000 cells from normal human liver tissue to construct a human liver cell atlas. We reveal previously unknown subtypes in different cell type compartments. We also use our normal liver cell atlas to infer perturbed phenoytpes of cells from HCC samples, human cells engrafted into a mouse liver and liver organoids.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 319 Samples
FTP download: GEO (CSV, RDATA, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124395/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA511895
Series		Accession: GSE124395	ID: 200124395

473. Expression Profiling of Cisplatin Resistant IGROV1 Cell Lines vs. Wild Type IGROV1 Cell Lines
(Submitter supplied) Ovarian cancer IGROV1 cells were studied to profile the expression of wild type (WT, Cisplatin Susceptible) cells and Cisplatin Resistant (CR) cells. The goal was to gain insights or to build hypotheses into the mechanisms of Cisplatin resistance in this cell-based model.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115939/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476559
Series		Accession: GSE115939	ID: 200115939

474. The MybMuvB complex is required for YAP dependent transcription of mitotic genes
(Submitter supplied) YAP/TAZ, downstream effectors of the Hippo pathway, are important regulators of proliferation. Here we show that the ability of YAP to activate mitotic gene expression is dependent on the Myb-MuvB (MMB) complex, a master regulator of genes expressed in the G2/M phase of the cell cycle. By carrying out genome-wide expression and binding analyses, we found that YAP promotes binding of the MMB subunit B-MYB to the promoters of mitotic target genes. more...
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 33 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115787/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476018
Series		Accession: GSE115787	ID: 200115787

475. RNAseq data of 81 liver cancer cell lines
(Submitter supplied) A large panel of 81 liver cancer cell models, designated as LIver cancer MOdel REpository (LIMORE) was constructed. These cell lines include 31 public cell lines and 50 new cell models establishend from Chinese liver cancer patients. Whole genome sequencing (WGS), exome sequencing (WES) and RNA sequencing (RNAseq) were performed to obtain the genetic information for these cell lines. These cell lines and associated data provide new models and also a rich resource for liver cancer.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL11154 GPL20795 73 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97098/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA380668
Series		Accession: GSE97098	ID: 200097098

476. lncRNA n384546 promotes thyroid papillary cancer proliferation and migration by targeting miR-145-5p to regulate AKT3
(Submitter supplied) we document a novel lncRNA, n384546, which may exert its oncogenic property in PTC tumorigenesis by sponging miR-145-5p and then regulating its target AKT3.This study reveals that n384546 is an oncogenic lncRNA in human thyroid cancer.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124841/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA513972
Series		Accession: GSE124841	ID: 200124841

477. Zika virus antagonizes interferon response in patients and disrupts RIG-I-MAVS interaction through its CARD-TM domains
(Submitter supplied) The emerging threat to global health associated with the Zika virus (ZIKV) epidemics and its link to severe complications highlights a growing need to better understand the pathogenic mechanisms of ZIKV.  Accumulating evidence for a critical role of type I interferon (IFN-I) in protecting hosts from ZIKV infection lies in the findings that ZIKV has evolved various strategies to subvert the host defense line by counteracting the early IFN induction or subsequent IFN signaling. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123835/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510012
Series		Accession: GSE123835	ID: 200123835

478. Cytokeratin 18 knockdown decreases cell apoptosis by regulating the transcription and alternative splicing in Hela cell
(Submitter supplied) Cytokeratin 18(CK18), one of the major components of intermediate filaments (IF) in simple-type epithelial cells, has been used as the biomarker of several cancers. CK18 has been also reported to be dysregulated in cervical cancers, however, the precise molecular pathways regulated by CK18 remained elusive. In this study, CK18 was knockdown in Hela cells and which led to a significantly decrease of cell apoptosis compared with control cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119255/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488613
Series		Accession: GSE119255	ID: 200119255

479. SULT2B11b regulates sensitivity to TNF-mediated cell death in Prostate Cancer
(Submitter supplied) Single-cell mRNA sequencing (scRNA-seq) study was conducted to compare the transcriptomes of SULT2B1b knockdown (KD) versus non-targeting (Control) KD LNCaP cells.  Over 2,000 differentially expressed (DE) genes were identified along with alterations in numerous canonical pathways, including the death receptor signaling pathway.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 414 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117410/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482003
Series		Accession: GSE117410	ID: 200117410

480. Exploiting an Asp-Glu "switch" in glycogen synthase kinase 3 to design paralog selective inhibitors for use in acute myeloid leukemia
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 15 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109987/
Series		Accession: GSE109987	ID: 200109987

481. Genome-wide transcriptional profile for the GSK3β selective inhibitor BRD3731
(Submitter supplied) Exploiting an Asp-Glu “switch” in glycogen synthase kinase 3 to design paralog selective inhibitors for use in acute myeloid leukemia: Genome-wide transcriptional profile for the GSK3β selective inhibitor BRD3731. Glycogen synthase kinase 3 (GSK3), a key regulatory kinase in the WNT pathway, remains a therapeutic target of interest in many diseases. While dual GSK3α/β inhibitors have entered clinical trials, none has successfully translated to clinical application. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109986/
Series		Accession: GSE109986	ID: 200109986

482. Genome-wide transcriptional profiles for the GSK3α selective inhibitor BRD0507 and for the GSK3α/β dual inhibitor BRD0320
(Submitter supplied) Exploiting an Asp-Glu “switch” in glycogen synthase kinase 3 to design paralog selective inhibitors for use in acute myeloid leukemia: Genome-wide transcriptional profiles for the GSK3α selective inhibitor BRD0507 and for the GSK3α/β dual inhibitor BRD0320 Glycogen synthase kinase 3 (GSK3), a key regulatory kinase in the WNT pathway, remains a therapeutic target of interest in many diseases. While dual GSK3α/β inhibitors have entered clinical trials, none has successfully translated to clinical application. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109985/
Series		Accession: GSE109985	ID: 200109985

483. A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification
(Submitter supplied) Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and is a key contributor to both normal developmental processes and disease states. While cost-effective and accurate for quantification, short-read RNA-seq lacks the ability to resolve full-length transcript isoforms despite increasingly sophisticated computational methods. Long-read sequencing platforms such as Pacific Biosciences (PacBio) and Oxford Nanopore (ONT) bypass the transcript reconstruction challenges of short-reads. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24106 8 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132766/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA548942
Series		Accession: GSE132766	ID: 200132766

484. Comparison of RhoE and RhoEα regulated pathways
(Submitter supplied) We identified a new RhoE isoform, RhoEα, and compared the differentially regulated signalings by these two proteins. Both RhoE and RhoEα were first knocked out via CRISPR/Cas9 in HEK 293 cells and HeLa cells (KO cells), followed by RhoE and RhoEα reintroduction (RhoE reintroduction cells and RhoEα reintroduction cells, resepectively). Wild-type cells, KO cells, RhoE reintrocution cells, and RhoEα reintroduction cells were then subjected to RNA-seq analysis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 8 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132718/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA548801
Series		Accession: GSE132718	ID: 200132718

485. RNAseq of prostate cancer cells (PC3 and DU145)  treated with 2.5 uM pentamidine or vehicle
(Submitter supplied) To uncover the mechanism underlying the effect of pentamidine on prostate cancer cells, we performed RNA sequencing (RNA-seq) to compare the transcriptional difference between pentamidine- and vehicle-treated prostate cancer cells (PC3 and DU145 cells).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132693/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA548765
Series		Accession: GSE132693	ID: 200132693

486. Identification of transcription start sites for human A549 cell line using ReCappable-seq
(Submitter supplied) We develop a method Re-Cappable-seq for determining eukaryotic transcription start sites derived from all RNA polymerases at nucleotide resolution. In particular, this method identifies the Pol-I and Pol-III TSSs, which are missing by CAGE. Applied to human A549 cell line, our method results in the identification of 33,468 and 5,269 high confidence Pol-II and non-Pol-II TSS respectively. Re-Cappable-seq identifies Pol-II TSS with higher specificity than CAGE.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (GTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132660/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA548673
Series		Accession: GSE132660	ID: 200132660

487. Functional Comparison of the HGF/Met and MSP/Ron Systems in a Pancreatic Cancer Model
(Submitter supplied) Pancreatic cancer is an aggressive disease with a poor prognosis for which current standard chemotherapeutic treatment options offer little survival benefit. In recent years, receptor tyrosine kinases (RTK)s have garnered interest as therapeutic targets to augment or replace standard chemotherapeutic therapies because of their high expression levels in various cancers and their ability to promote cell growth, migration, and survival. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 18 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129075/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529910
Series		Accession: GSE129075	ID: 200129075

488. Landscapes of gene translation in hepatocellular carcinoma tumors revealed by ribosome profiling
(Submitter supplied) Despite the critical role of translation in the multi-level gene expression regulation program that controls the protein abundance, a high-resolution view on the landscapes of gene translation in cancer has been missing. We used the technique of ribosome profiling to dissect the translatomes of human liver tumors and their adjacent normal tissues. Our results, as a novel resource, revealed genome-wide abnormalities of translation efficiencies in tumors and context-dependent non-canonical ORFs.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 40 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112705/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448763
Series		Accession: GSE112705	ID: 200112705

489. MITF controls the TCA cycle to modulate the melanoma hypoxia response
(Submitter supplied) In response to the dynamic intra-tumor microenvironment, melanoma cells adopt different phenotypic states possessing distinct biological properties associated with differential expression of the microphthalmia-associated transcription factor (MITF). The response to hypoxia, a major microenvironmental cue, is underpinned by expression of hypoxia-inducible transcription factors (HIFs) that reprogram metabolism and promote pro-angiogenic VEGF expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 36 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132624/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA548550
Series		Accession: GSE132624	ID: 200132624

490. Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL24676 GPL16791 GPL15520 1252 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111898/
Series		Accession: GSE111898	ID: 200111898

491. Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer [ 10x genomics]
(Submitter supplied) High numbers of tissue-resident memory T (TRM) cells have been associated with better clinical outcomes in cancer patients. However, the molecular characteristics that drive their efficient immune response to tumors are poorly understood. Here, using single-cell and bulk transcriptomic analysis of purified populations of TRM   and non-TRM cells we characterise these populations
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111896/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438507
Series		Accession: GSE111896	ID: 200111896

492. Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer [scRNA-seq]
(Submitter supplied) High numbers of tissue-resident memory T (TRM) cells have been associated with better clinical outcomes in cancer patients. However, the molecular characteristics that drive their efficient immune response to tumors are poorly understood. Here, using single-cell and bulk transcriptomic analysis of purified populations of TRM   and non-TRM cells we characterise these populations
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 1084 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111894/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438494
Series		Accession: GSE111894	ID: 200111894

493. Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer [ bulk RNA-seq]
(Submitter supplied) High numbers of tissue-resident memory T (TRM) cells have been associated with better clinical outcomes in cancer patients. However, the molecular characteristics that drive their efficient immune response to tumors are poorly understood. Here, using single-cell and bulk transcriptomic analysis of purified populations of TRM   and non-TRM cells we characterise these populations
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 133 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111892/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438495
Series		Accession: GSE111892	ID: 200111892

494. Transcriptome Signature of Cellular Senescence
(Submitter supplied) Abstract: Cellular senescence, an integral component of aging and cancer, arises in response to diverse triggers, including telomere attrition, macromolecular damage, and signaling from activated oncogenes.  At present, senescent cells are identified by the combined presence of multiple traits, such as senescence-associated protein expression and secretion, DNA damage, and β-galactosidase activity; unfortunately, these traits are neither exclusively nor universally present in senescent cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 37 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130727/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA541183
Series		Accession: GSE130727	ID: 200130727

495. Tumor- and cytokine-primed human natural killer cells exhibit distinct phenotypic and transcriptional signatures [RNA-seq]
(Submitter supplied) An emerging cellular immunotherapy for cancer is based on the cytolytic activity of natural killer (NK) cells against a wide range of tumors. Although in vitro activation or ‘priming’ of NK cells by exposure to pro-inflammatory cytokines such as interleukin (IL)-2 has been extensively studied, the biological consequences of NK cell activation in response to target cell interactions are less characterized. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130284/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA534526
Series		Accession: GSE130284	ID: 200130284

496. Cistromic re-programming by truncating GATA3 mutations promotes mesenchymal transformation in vitro, but not mammary tumour formation in mice
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 34 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122849/
Series		Accession: GSE122849	ID: 200122849

497. Cistromic re-programming by truncating GATA3 mutations promotes mesenchymal transformation in vitro, but not mammary tumour formation in mice [RNA-seq]
(Submitter supplied) Heterozygous mutations in the transcription factor GATA3 are identified in 10-15% of all breast cancer cases. Most of these are protein-truncating mutations, concentrated within or downstream of the second GATA-type zinc-finger domain. Here, we investigated the functional consequences of expression of two truncated GATA3 mutants, in vitro in breast cancer cell lines and in vivo in the mouse mammary gland. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122848/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506684
Series		Accession: GSE122848	ID: 200122848

498. Spatial chromosome folding and active transcription drive DNA fragility and formation of oncogenic MLL translocations
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL18573 GPL20301 20 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121742/
Series		Accession: GSE121742	ID: 200121742

499. Spatial chromosome folding and active transcription drive DNA fragility and formation of oncogenic MLL translocations [RNA-Seq]
(Submitter supplied) How spatial chromosome organization influences genome integrity is still poorly understood. Here we show that DNA double-strand breaks (DSBs) mediated by topoisomerase 2 (TOP2) activities, are enriched at chromatin loop anchors with high transcriptional activity. Recurrent DSBs occur at CTCF/cohesin bound sites at the bases of chromatin loops and their frequency positively correlates with transcriptional output and directionality. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121741/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA498294
Series		Accession: GSE121741	ID: 200121741

500. Developmental enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors
(Submitter supplied) Most pancreatic neuroendocrine tumors (PNETs) do not produce symptoms of hormonal excess and are hence considered ‘non-functional’. Their clinical behaviors vary widely, emphasizing the need for a robust classification with prognostic power. Using enhancer maps to infer regulatory programs, we find that the large majority of non-functional PNETs fall into two major sub-types –A and B– that reflect alpha and beta endocrine cell ontogeny, respectively. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL18573 79 Samples
FTP download: GEO (BED, BW, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116356/
Series		Accession: GSE116356	ID: 200116356

501. The hypoxic landscape of melanoma
(Submitter supplied) Micro-environment played an important role in the disease progression and overall survival. More recently, hypoxic signature were identified as one of the key signatures of innate anti-PD1 resistance, however, relatively little had been done to identify the key molecular signature of hypoxic response in melanoma and how these may correlated with other know signatures which correlate with poor prognosis. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 42 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95280/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376554
Series		Accession: GSE95280	ID: 200095280

502. Estrogen-independent molecular actions of mutant estrogen receptor alpha in endometrial cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 58 Samples
FTP download: GEO (BEDGRAPH, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132430/
Series		Accession: GSE132430	ID: 200132430

503. Estrogen-independent molecular actions of mutant estrogen receptor alpha in endometrial cancer [RNA-seq]
(Submitter supplied) Estrogen receptor alpha (ESR1) mutations have been identified in hormone therapy resistant breast cancer and primary endometrial cancer. Analyses in breast cancer suggests that mutant ESR1 exhibits estrogen independent activity. In endometrial cancer, ESR1 mutations are associated with worse outcomes and less obesity, however experimental investigation of these mutations has not been performed. Using a unique CRISPR/Cas9 strategy, we introduced the D538G mutation, a common endometrial cancer mutation that alters the ligand binding domain of ESR1, while epitope tagging the endogenous locus. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132428/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA548070
Series		Accession: GSE132428	ID: 200132428

504. Tumor- and cytokine-primed human natural killer cells exhibit distinct phenotypic and transcriptional signatures
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing
Platforms: GPL23816 GPL18573 24 Samples
FTP download: GEO (RCC) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130286/
Series		Accession: GSE130286	ID: 200130286

505. HDAC inhibition enhances the in vivo efficacy of MEK inhibitor therapy in uveal melanoma
(Submitter supplied) Purpose: The clinical use of MEK inhibitors in uveal melanoma is limited by the rapid acquisition of resistance. The current study has used unbiased multi-omics and drug screens to identify the pan-HDAC inhibitor panobinostat as an effective strategy to limit MEK inhibitor resistance.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127948/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA525852
Series		Accession: GSE127948	ID: 200127948

506. Gene expression from AsPC-1 cells treated with PTC596 and DMSO
(Submitter supplied) This study examines the transcriptional changes invoked by the novel anti-cancer agent PTC596 in AsPC-1 pancreatic cancer cells as compared to DMSO.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118441/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485679
Series		Accession: GSE118441	ID: 200118441

507. CRKL regulates alternative splicing of genes that function in tumorigenesis and cancer progression
(Submitter supplied) CRKL adaptor protein was demonstrated to have important effects in various types of human cancer and contributes to malignant cell growth and chemoresistance as an overexpressed oncoprotein in cervical carcinoma. But the special molecular mechanisms of CRKL in cervical cancer remain unknown. Here we reported that CRKL regulates genes in cervical cancer related pathways via targeting alternative splicing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120631/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA495833
Series		Accession: GSE120631	ID: 200120631

508. MenSCs inhibit HCC growth through oncogenic pathway suppression via regulating 5-hmC in enhancer elements
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL20301 22 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120160/
Series		Accession: GSE120160	ID: 200120160

509. MenSCs inhibit HCC growth through oncogenic pathway suppression via regulating 5-hmC in enhancer elements [RNA-seq]
(Submitter supplied) We utilize MeDIP-seq, hMeDIP-seq and RNA-seq technologies to explore the epigenetic alterations in HCC after MenSC therapy. We provide distinct epigenetic landscapes of HCC cells mediated by MenSCs and demonstrate that MenSCs exert anticancer functions by regulating 5-hmC and 5-mC abundance in enhancer and promoter regions of oncogenic pathways. Deactivation of PI3K/AKT and RAF/ERK signaling attenuated the inhibition of FOXO3 and promoted downstream apoptosis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120158/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA491746
Series		Accession: GSE120158	ID: 200120158

510. Genome-wide analysis of ferroptosis related genes in liver cancer cells.
(Submitter supplied) To seek ferroptosis related genes in liver cancer cells, we treated HepG2 cells using ferroptosis inducer Erastin and inhibitor Ferrostatin, respectively. We found that a subset of genes were up-regulated in Erastin treatment groups and down-regulated in Ferrostatin treatment groups, suggesting that these genes might be correlated with ferroptosis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104462/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA412671
Series		Accession: GSE104462	ID: 200104462

511. Small cell lung cancer PDX model response to LSD1 inhibitor RG6016/ORY1001
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103097/
Series		Accession: GSE103097	ID: 200103097

512. Comparison of small cell lung cancer PDX model FHSC04 for response to LSD1 inhibitor RG6016/ORY1001
(Submitter supplied) The goal of this study was to understand how the LSD1 inhibitor RG6016/ORY1001 leads to selective efficacy in subsets of small cell lung cancer. SCLC cell lines, PDX models studied ex vivo and studied in vivo were employed in this analysis
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103096/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA400280
Series		Accession: GSE103096	ID: 200103096

513. Comparison of 7 small cell lung cancer PDX models, cultured ex vivo, for response to LSD1 inhibitor RG6016/ORY1001
(Submitter supplied) The goal of this study was to understand how the LSD1 inhibitor RG6016/ORY1001 leads to selective efficacy in subsets of small cell lung cancer. SCLC cell lines, PDX models studied ex vivo and studied in vivo were employed in this analysis
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103095/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA400281
Series		Accession: GSE103095	ID: 200103095

514. Mixed tailing by TUT3 and TUT5 shields mRNA from rapid deadenylation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Drosophila melanogaster; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL17275 GPL16791 29 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116355/
Series		Accession: GSE116355	ID: 200116355

515. Mixed tailing by TUT3 and TUT5 shields mRNA from rapid deadenylation [TAIL-Seq]
(Submitter supplied) RNA tails play integral roles in the control of mRNA translation and decay. Guanylation of poly(A) tail was discovered recently, yet the enzymology and function remain obscure. Here we identify TUT3 (PAPD5) and TUT5 (PAPD7) (TUT3/5) as the enzymes responsible for mRNA guanylation. Purified TUT3/5 predominantly incorporate GTPs to generate a mixed poly(A) tail with intermittent non-adenosine residues. more...
Organism:	Homo sapiens; Drosophila melanogaster
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17275 GPL16791 25 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116349/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA478242
Series		Accession: GSE116349	ID: 200116349

516. Mixed tailing by TUT3 and TUT5 shields mRNA from rapid deadenylation [RNA-Seq]
(Submitter supplied) RNA tails play integral roles in the control of mRNA translation and decay. Guanylation of poly(A) tail was discovered recently, yet the enzymology and function remain obscure. Here we identify TUT3 (PAPD5) and TUT5 (PAPD7) (TUT3/5) as the enzymes responsible for mRNA guanylation. Purified TUT3/5 predominantly incorporate GTPs to generate a mixed poly(A) tail with intermittent non-adenosine residues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115529/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475275
Series		Accession: GSE115529	ID: 200115529

517. Gene expression profile of HGC27 and LMSU gastric cancer cell p53 KO and KD
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 20 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132334/
Series		Accession: GSE132334	ID: 200132334

518. Gene expression profile of HGC27 gastric cancer cell p53 KO and KD
(Submitter supplied) HGC27 gastric cancer cells were manipulated to express mutant p53
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132333/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA547629
Series		Accession: GSE132333	ID: 200132333

519. Gene expression profile of LMSU gastric cancer cell p53 KO and KD
(Submitter supplied) LMSU gastric cancer cells were manipulated to either knockout or knockdown mutant p53-R175H, which is endogenously mutated and expressed in this cell line.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132331/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA547627
Series		Accession: GSE132331	ID: 200132331

520. Gene expression profile of hepatocellular carcinoma with marked immune cell infiltration II
(Submitter supplied) Tumor microenvironmental characteristics using gene expression profiles in hepatocellular carcinoma  with marked immune stroma (HCC-IS) compared to conventional hepatocellular carcinoma (C-HCC).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124752/
Series		Accession: GSE124752	ID: 200124752

521. Gene expression profile of hepatocellular carcinoma with marked immune cell infiltration I
(Submitter supplied) Tumor microenvironmental characteristics using gene expression profiles in hepatocellular carcinoma  with marked immune stroma (HCC-IS) compared to conventional hepatocellular carcinoma (C-HCC).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 206 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124751/
Series		Accession: GSE124751	ID: 200124751

522. RNA-seq of HCT116 and HCT116-DKO colon cancer cell lines
(Submitter supplied) RNA-seq was performed on parental HCT116 colon cancer cell line and on HCT116 DKO (double knock-out) cell line, which contains genetic knockouts of both DNA methyltransferases DNMT1 (-/-) and DNMT3b (-/-).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82338/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324686
Series		Accession: GSE82338	ID: 200082338

523. Ex vivo screen identifies CDK12 as a metastatic vulnerability in osteosarcoma
(Submitter supplied) Despite progress in intensification of therapy, outcomes for patients with metastatic osteosarcoma (OS) have not improved in thirty years. We developed a system that enables preclinical screening of compounds against metastatic OS cells in the context of the native lung microenvironment.  Using this strategy to screen a library of epigenetically-targeted compounds, we identified inhibitors of CDK12 to be most effective, reducing OS cell outgrowth in the lung by >90% at sub-micromolar doses. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL16791 GPL24676 34 Samples
FTP download: GEO (BROADPEAK, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132233/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA546568
Series		Accession: GSE132233	ID: 200132233

524. Genomic Signatures Reveal DNA Damage Response Deficiency in Brain Metastases of Colorectal Cancer
(Submitter supplied) We performed RNA-Seq on primary colorectal cancer (CRC) tissues and brain metastatic tissues from two CRC patients. Differential expression analysis was conducted to find genes associated with brain metastasis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132226/
Series		Accession: GSE132226	ID: 200132226

525. The expression profiles of GBC liver metastasis
(Submitter supplied) In order to analyze the differential profile of RNAs from patients with liver metastasis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132223/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA546548
Series		Accession: GSE132223	ID: 200132223

526. The secretome of skin cancer cells activates the mTOR/MYC pathway in healthy keratinocytes and converts them into tumorigenic cells
(Submitter supplied) Cutaneous squamous cell carcinoma (cSCC) is the most aggressive tumor among non-melanoma skin cancers (NMSC), showing a high potential for local invasion and metastasis. In recent years, the incidence of cSCC has increased tremendously due to increased UV exposure. The secretome of cancer cells is currently the focus of many studies in order to identify new marker proteins for different types of cancer and to investigate its influence on the tumor microenvironment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132215/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA546533
Series		Accession: GSE132215	ID: 200132215

527. Exploring ILF2 regulatory genes by next-generation sequencing
(Submitter supplied) We knocked down the expression of ILF2 in the A549 cell line and sequenced the RNA genes with the untreated A549 cells to find the regulatory gene of ILF2.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126475/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA522000
Series		Accession: GSE126475	ID: 200126475

528. RNA-Seq analysis of prostate cancer cell line LNCaP treated with vehicle, androgen, androgen and IMTPPE, androgen and JJ-(+)-450, androgen and JJ-(-)450, androgen and enzalutamide
(Submitter supplied) RNA-Seq analysis of prostate cancer cell line LNCaP treated with vehicle (C), androgen (R), androgen and IMTPPE (R + IMTPPE), androgen and JJ-(+)-450 (androgen + (-)450), androgen and JJ-(-)450 (androgen + (-)450), androgen and enzalutamide (androgen +Enz). To evaluate if our compounds can inhibit AR function specifically and completely, LNCaP mRNA profiles of cells treated with IMTPPE, (+)-JJ-450 and (-)-JJ-450, comparing to enzalutamide. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115395/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474819
Series		Accession: GSE115395	ID: 200115395

529. Global altered gene expression in  triple-negative breast cancer tumor samples treated with CDK2 and EZH2 inhibitors
(Submitter supplied) Triple-negative breast cancer cell line SUM-149 xenograft mouse model was treated with CDK2 inhibitor (dinaciclib) and EZH2 inhibitor (EPZ6438) for 10 days to examine global transcriptome alternations by RNAseq. Expression levels of more than 801 and  741 gene were altered by CDK2 inhibitor and EZH2 inhibitor treatment, respectively.Among differential changed genes induced by CDK2 inhibitor and EZH2 inhibitor, we defined top 109 common up- and down-regulated gene sets in the inhibitor-treated tumors.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132194/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA546291
Series		Accession: GSE132194	ID: 200132194

530. Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells
(Submitter supplied) Intra-tumor genetic heterogeneity comes from whole chromosome and/or focal copy number variations (CNVs).  We investigated the impact of whole chromosome CNVs on gene expression by performing single-cell RNA sequencing on a chromosomally unstable glioblastoma cancer stem cell (CSC) line and a control normal, diploid neural stem cell (NSC) line.  From the gene expression data, we computationally inferred large-scale CNVs in single cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21697 134 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132172/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA546254
Series		Accession: GSE132172	ID: 200132172

531. Ribosome queuing enables non-AUG translation to be resistant to multiple protein synthesis inhibitors
(Submitter supplied) Aberrant translation initiation at non-AUG start codons is associated with multiple cancers and neurodegenerative diseases. Nevertheless, how non-AUG translation is regulated differently from canonical translation is poorly understood. We thus used start codon-selective  reporters and ribosome profiling to characterize how translation from non-AUG start codons responds to protein synthesis inhibitors in human cells. more...
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (CSV, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125086/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515197
Series		Accession: GSE125086	ID: 200125086

532. Identification of Host Biomarkers of EBV Latency IIb and Latency III
(Submitter supplied) Deciphering the molecular pathogenesis of virally induced cancers is challenging due, in part, to the heterogeneity of both viral and host gene expression. Epstein-Barr Virus (EBV) is a ubiquitous herpesvirus prevalent in B-cell lymphomas of the immune suppressed. EBV infection of primary human B cells leads to their immortalization into lymphoblastoid cell lines (LCLs) serving as a model of these lymphomas. more...
Organism:	Homo sapiens; Human gammaherpesvirus 4
Type:		Expression profiling by high throughput sequencing
Platform: GPL23362 16 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132138/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA546009
Series		Accession: GSE132138	ID: 200132138

533. Transcriptome regulation by ALK in cerebral organoids revealed by single-cell RNA sequencing
(Submitter supplied) Cerebral organoids derived from human pluripotent stem cells has been used as a model to study the development of mammalian brain. In this study, we employed 10x genomic single-cell RNA sequencing analysis to gain mechanical insight into the transcriptional changes of cells in cerebral organoids subject to the regulation by anaplastic lymphoma kinase (ALK) pathway. Based on the marker genes that most strongly contribute to the clusters, we annotated each cluster to cell types including radial glial cells (RGCs, SOX2 dominant), RGCs and intermediate progenitors (IPs, both SOX2 and EOMES positive), proliferating cells (Ki67 positive), early-born neurons (TBR1 and BCL11B dominant) and immature neurons (both SOX2 and TBR1/BCL11B/POU3F2 positive). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132105/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA545955
Series		Accession: GSE132105	ID: 200132105

534. A transcriptome dataset revealing the molecular features of breast cancer stem cells
(Submitter supplied) Triple negative breast cancers lack targeted therapies with little side effects and contain higher percentage of cancer stem cells than the other breast cancer subtypes. Genes capturing the features of cancer stem cells of such diseases may serve as potential subtyping marker or therapeutic targets for triple negative breast cancer management. This data descriptor presents a set of transcriptome data from 3 cohorts of cancer stem cells as represented as CD44+/CD24-/low and 2 cohorts of non-cancer stem cells isolated from triple negative breast cancer cells, each having 3 replicates.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132083/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA545898
Series		Accession: GSE132083	ID: 200132083

535. RNA-seq of tumor cells following angiopellosis extravasation
(Submitter supplied) Tumor cells were observed to undergo extravasation through intrivital imaging and immediately following the extravasation they were isolated and compared to control cells using RNA-seq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132082/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA545897
Series		Accession: GSE132082	ID: 200132082

536. RNA sequence analysis of stable versus reversible EMT events and the resultant metastases
(Submitter supplied) The ability of breast cancer cells to transiently transition between epithelial and mesenchymal states is critical to complete the metastatic process. In contrast, induction of epithelial-mesenchymal transition (EMT) through the acquisition of drug persistence is a more stable event. Herein, we utilize Her2 transformed human mammary epithelial (HMLE) cells to compare a reversible model of EMT induced by TGF-beta to a stable mesenchymal phenotype induced by chronic exposure to the ErbB kinase inhibitor, lapatinib. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115255/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474381
Series		Accession: GSE115255	ID: 200115255

537. E2F6-mediated ceRNA and epigenetic silencing of miR-193a promote cancer stemness and immunoevasion in ovarian cancer
(Submitter supplied) To investigate the knockdown effect of EZH2 and E2F6, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by the knockdown of EZH2 or E2F6 in CP70 ovarian cancer cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109184/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA430071
Series		Accession: GSE109184	ID: 200109184

538. CATACOMB: an endogenous inducible gene that antagonizes H3K27 methylation activity of Polycomb Repressive complex 2 via a H3K27M-like mechanism
(Submitter supplied) Dysregulation of Polycomb Repressive Complex 2 (PRC2) function is a common feature of many cancer types, including both solid and hematological malignancies. A number of chromosomal translocations involving Polycomb group proteins have been identified, however, the molecular function of these fusion proteins remains largely unexplored. Here we characterize two endometrial stromal sarcoma (ESS) associated fusion proteins: JAZF1-SUZ12 and MBTD1- CXORF67. more...
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL24676 18 Samples
FTP download: GEO (BW, COV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131626/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA544242
Series		Accession: GSE131626	ID: 200131626

539. IRF2BP2 Modulates the Crosstalk between Glucocorticoid and TNF Signaling
(Submitter supplied) Here we have analyzed the role of interferon regulatory factor-2 binding protein-2 (IRF2BP2) in glucocorticoid and tumor necrosis factor alpha (TNF) signaling. We used ChIP-seq to analyze chromatin binding of IRF2BP2 in glucocorticoid (dexamethasone, dex) and vehicle treated HEK293 cells expressing GR (HEK293-GR). Furthermore, we used RNA-seq to analyze how silencing of IRF2BP2 modulates transcriptional responses to dex treatment in HEK293-GR cells, and dex, TNF and co-treatment (dex and TNF, DT) in A549 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 44 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124636/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512883
Series		Accession: GSE124636	ID: 200124636

540. Generating Patterned Kidney Organoids for Studying Development and Diseases [scRNA-Seq]
(Submitter supplied) Human pluripotent stem cells (hPSCs)-derived kidney organoids recapitulate complex developmental processes and tissue architectures, but the intrinsic limitations, such as variability and a lack of vasculature, have greatly hampered their application. Here we establish a highly efficient and versatile protocol for generating vascularized three-dimensional (3D) kidney organoids. We employ dynamic modulation of WNT signaling to control the relative proportion of proximal versus distal nephron segments, thereby producing a correlative level of VEGFA to define the resident vascular network. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE132nnn/GSE132023/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA545652
Series		Accession: GSE132023	ID: 200132023

541. Profiling of protrusion-enriched RNAs from human breast cancer cell line MDA-MB-231
(Submitter supplied) The goals of this study are to compare the gene expression of cell protrusions and corresponding cell bodies by isolating cell protrusions from cultured MDA-MB-231 cells in a novel microfluidic device.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 10 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130271/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA534487
Series		Accession: GSE130271	ID: 200130271

542. PAX5 promotes progression of neuroendocrine prostate cancer
(Submitter supplied) Analysis of prostate adnocarcinoma cell line LNCaP cells overexpression pair box 5 (PAX5) for up to 4 days. The goals of this study are to compare PAX5 overexpression in LNCaP cell drives transcriptome profiling (RNA-seq) changes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129887/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA533095
Series		Accession: GSE129887	ID: 200129887

543. PCIF1 catalyzes m6Am mRNA methylation to regulate gene expression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 57 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122803/
Series		Accession: GSE122803	ID: 200122803

544. Pro-Seq of MEL624 control and PCIF1 KO cells
(Submitter supplied) We analyzed human melanoma cells by PRO-Seq in order to determine the effect of PCIF1 KO in Pol II dynamics
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122802/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506412
Series		Accession: GSE122802	ID: 200122802

545. m6A MeRIP-Seq of MEL624 control and PCIF1 KO cells
(Submitter supplied) We analyzed m6A distribution by m6A MeRIP in otder to determine the effect of PCIF1 KO over m6A distribution in human melanoma cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122801/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506411
Series		Accession: GSE122801	ID: 200122801

546. m6Am-Exo-Seq mapping of MEL624 control and PCIF1 KO cells
(Submitter supplied) We analyzed m6Am distribution by m6Am-Exo-Seq in order to determine the mRNAs marked by m6Am in human melanoma cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 30 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122800/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506410
Series		Accession: GSE122800	ID: 200122800

547. De novo assembled individual genome does not show advantage against standard reference genome: a demonstration of Chinese Han Population
(Submitter supplied) We compared standard human reference genome GRCh38 and de novo assembled reference genome HX1 in precision medicine applications for specific ethnics. In order to quantify the HX1 misassembled genes and HX1-specific contigs, we performed RNA-seq and RNC-seq on hepatocellular carcinoma cell lines (MHCC97H, MHCCLM3 and MHCCLM6) which were derived from Chinese Han individuals. In which, RNC-seq datasets of MHCC97H and MHCCLM3 had been published. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121013/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA495351
Series		Accession: GSE121013	ID: 200121013

548. Single-Cell Genotyping of Transcriptomes
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL16791 GPL22245 GPL15520 28 Samples
FTP download: GEO (MTX, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117826/
Series		Accession: GSE117826	ID: 200117826

549. RNA-seq of Single-Cell Genotyping of Transcriptomes
(Submitter supplied) Somatic cancer driver mutations may result in distinctly diverging phenotypic outputs. Thus, a common driver lesion may result in cancer subtypes with distinct clinical presentations and outcomes. The diverging phenotypic outputs of mutations result from the superimposition of the mutations with distinct progenitor cell populations that have differing lineage potential. However, our ability to test this hypothesis has been challenged by currently available tools. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL22245 GPL16791 12 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117824/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483241
Series		Accession: GSE117824	ID: 200117824

550. OGT knockout S2VP10 cells
(Submitter supplied) Pancreatic Cancer cells were transfected with CRISR based OGT knockouts
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 24 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114472/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471509
Series		Accession: GSE114472	ID: 200114472

551. hnRNPC regulates cancer-specific alternative cleavage and polyadenylation profiles
(Submitter supplied) Alternative cleavage and polyadenylation (APA) can occur at more than half of all human genes, greatly enhancing the cellular repertoire of mRNA isoforms. As these isoforms can have altered stability, localisation and coding potential, deregulation of APA can disrupt gene expression and this has been linked to many diseases including cancer progression. How APA generates cancer-specific isoform profiles and what their physiological consequences are, however, is largely unclear. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 32 Samples
FTP download: GEO (BIGWIG, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102357/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397552
Series		Accession: GSE102357	ID: 200102357

552. Sequencing Facilitates Quantitative Analysis of gene expression among 3 stromal cell populations: NAF, CAF, CAF_HiP
(Submitter supplied) Purpose : Primary cultured fibroblast cultures can be classified based on their tumor promoting ability. Normal associated fibroblasts (NAF) cannot transform benign epithelia. Cancer associated fibroblasts  (CAF) can transform benign epithelia into cancer. As described in Kato and Placencio et al., High passage CAF (CAF_HiP) cells have lost the ability to potentiate tumor growth. This study sought to identify the differences among three groups of fibroblasts: NAF, CAF, and CAF_HiP Methods :Human male prostatectomy tissues were cultured to generate primary cultured fibroblast cultures. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17301 3 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99744/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389465
Series		Accession: GSE99744	ID: 200099744

553. Selective Disruption of Core Regulatory Transcription
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL19415 GPL18573 107 Samples
FTP download: GEO (BED, HIC, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120771/
Series		Accession: GSE120771	ID: 200120771

554. Single-cell RNA sequencing of human kidney
(Submitter supplied) A comprehensive cellular anatomy of normal human kidney is vital to address the cellular origins of renal disease and renal cancer. Some kidney diseases may be cell type-specific, especially renal tubular cells. To investigate the classification and transcriptomic information of human kidney, we performed a method to obtain single-cell suspension of kidney rapidly, and conducted single-cell RNA sequencing (scRNA-seq). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 3 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131685/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA544431
Series		Accession: GSE131685	ID: 200131685

555. Identification of monocyte-like precursors of granulocytes as a mechanism for accumulation of PMN-MDSC in cancer
(Submitter supplied) Polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) inhibit immune responses in cancer, limit the effects of therapies and promote tumor cell metastasis. Here, we have identified a new precursor that differentiates into granulocytes in vitro and in vivo yet belong to the monocytic lineage. We have termed these cells monocyte-like precursors of granulocytes (MLPG). Under steady state conditions MLPG were absent in the spleen and barely detectable in the bone marrow (BM). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131552/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA544005
Series		Accession: GSE131552	ID: 200131552

556. DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation (RNA-seq)
(Submitter supplied) Enhancer elements are a key regulatory feature of many important genes. Several general features including the presence of specific histone modifications are used to demarcate potentially active enhancers. Here we reveal that putative enhancers marked with H3 lysine 79 (K79) di or trimethylation (me2/3) (which we name H3K79me2/3 enhancer elements or KEEs) can be found in multiple cell types. Mixed lineage leukemia gene (MLL) rearrangements (MLL-r) such as MLL-AF4 are a major cause of incurable acute lymphoblastic leukemias (ALL). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128632/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA528308
Series		Accession: GSE128632	ID: 200128632

557. Vitamin D and Wnt3A have additive and partially overlapping modulatory effects on gene expression and phenotype in human colon fibroblasts
(Submitter supplied) The Wnt/b-catenin signalling pathway is essential for intestinal epithelium homeostasis, but its aberrant activation is a hallmark of colorectal cancer (CRC). Several studies indicate that the bioactive vitamin D metabolite 1a,25-dihydroxyvitamin D3 (1,25(OH)2D3) inhibits proliferation and promotes epithelial differentiation of colon carcinoma cells in part through antagonism of the Wnt/b-catenin pathway. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120106/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA491666
Series		Accession: GSE120106	ID: 200120106

558. DOT1L inhibition reveals a distinct class of enhancers dependent upon H3K79 methylation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 63 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117865/
Series		Accession: GSE117865	ID: 200117865

559. Transcriptomic analysis of gastric cancer cells in response to stable over-expression of circular RNA derived from AGO2 gene (circAGO2)
(Submitter supplied) Argonaute 2 (AGO2) is the core component of microRNA (miRNA)-induced silencing complex, and plays a compelling role in tumorigenesis and aggressiveness. Recent studies have implicated the emerging roles of circular RNAs (circRNAs) in cancer progression. However, the roles of circRNAs in regulating the functions of AGO2 in cancer still remain elusive. We indentify one intronic circRNA derived from AGO2 gene (circAGO2) as a novel regulator of AGO2-miRNA complexes and cancer progression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114055/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA463893
Series		Accession: GSE114055	ID: 200114055

560. Quantitative profiling of the UGT transcriptome in human drug metabolizing tissues [Total RNA]
(Submitter supplied) Purpose: Maintenance of cellular homeostasis and xenobiotics detoxification relies on the glucuronidation pathway mediated by 19 human UDP-glucuronosyltransferase enzymes (UGTs) encoded by 10 highly homologous genes. Recent evidence suggests that alternative splicing largely expands the human UGT transcriptome. Results: we establish the quantitative portrait of the UGT transcriptome in major metabolic organs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82291/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324568
Series		Accession: GSE82291	ID: 200082291

561. Generating Patterned Kidney Organoids for Studying Development and Diseases [bulk RNA-Seq]
(Submitter supplied) Human pluripotent stem cells (hPSCs)-derived kidney organoids recapitulate complex developmental processes and tissue architectures, but the intrinsic limitations, such as variability and a lack of vasculature, have greatly hampered their application. Here we establish a highly efficient and versatile protocol for generating vascularized three-dimensional (3D) kidney organoids. We employ dynamic modulation of WNT signaling to control the relative proportion of proximal versus distal nephron segments, thereby producing a correlative level of VEGFA to define the resident vascular network. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131841/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA545106
Series		Accession: GSE131841	ID: 200131841

562. Transcriptomic analysis of effect of oncolytic measles virus (MV) on transformed and non-transformed bone marrow-derived mesenchymal stem cells (MSCs)
(Submitter supplied) The mechanisms by which oncolytic vaccine strains of measles virus exert their tumor selectivity are not well elucidated. The goal of this study is to compare the gene expression profiles of MV-resistant MSC cell line (hTERT) and MV-susceptible MSC cell line (5H) before and after infection with MV (24 hours post infection) Through RNA-seq we were able to identify genes that are potentially contribute to the resistant phenotype of hTERT cells compared to their malignant counterparts, 5H cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131840/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA545099
Series		Accession: GSE131840	ID: 200131840

563. Fractional Deletion of Compound Kushen Injection Indicates Cytokine Signaling Pathways are Critical for its Perturbation of the Cell Cycle
(Submitter supplied) We have used computational and experimental biology approaches to identify candidate mechanisms of action of a traditional Chinese medicine; Compound Kushen Injection (CKI), in a breast cancer cell line in which CKI has been shown to cause apoptosis. Because CKI is a complex mixture of plant secondary metabolites, we used a high-performance liquid chromatography (HPLC) fractionation and reconstitution approach to define chemical fractions required for CKI to induce apoptosis in MDA-MB-231 cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 54 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125743/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA517432
Series		Accession: GSE125743	ID: 200125743

564. Genome wide expression profiles (RNAseq) of human CD8+ T cells in resting, activated (CD3+CD28) and PD-1-stimulated cells (CD3+CD28+PD-L1-Fc) at diferent time points
(Submitter supplied) Background: Binding of the programmed death-1 (PD-1) receptor to its ligands (PD-L1/2) transduces inhibitory signals that promote exhaustion of activated T cells. Blockade of the PD 1 pathway is widely used for cancer treatment, yet the inhibitory signals transduced by PD-1 in T cells remain elusive. Methods: Expression profiles of human CD8+ T cells in resting, activated (CD3+CD28) and PD-1-stimulated cells (CD3+CD28+PD-L1-Fc) conditions were evaluated by RNA-seq. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122149/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA503833
Series		Accession: GSE122149	ID: 200122149

565. Selective Disruption of Core Regulatory Transcription [RNA-seq]
(Submitter supplied) Activation of identity determining transcription factors (TFs), or core regulatory TFs, is governed by cell-type specific enhancers, an important subset of these being super enhancers (SEs). This mechanism is distinct from constitutive expression of housekeeping genes. The characterization of drug-like small molecules to selectively inhibit core regulatory circuitry is of high interest for treatment of cancers, which are addicted to core regulatory TF function at SEs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 56 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121106/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA495665
Series		Accession: GSE121106	ID: 200121106

566. Acidification of tumor: stromal boundaries drive transcriptome alterations associated with aggressive phenotypes
(Submitter supplied) We report RNA splicing changes in response to extracellular acidification
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119646/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489852
Series		Accession: GSE119646	ID: 200119646

567. Gene amplification driven-long noncoding RNA SNHG17 regulates cell proliferation and migration in human non-small cell lung cancer
(Submitter supplied) Our findings indicated gene amplification driven-long noncoding RNA SNHG17 promotes cell proliferation and migration in NSCLC, suggesting its potential value as biomarker in NSCLC.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131543/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA543994
Series		Accession: GSE131543	ID: 200131543

568. MUC1-C represses the RASSF1A tumor suppressor and activated Kras signaling in human carcinoma cells
(Submitter supplied) RASSF1A encodes a tumor suppressor that inhibits RAS’RAF’MEK’ERK signaling and is one of the most frequently inactivated genes in human cancers. MUC1-C is an oncogenic effector of the cancer cell epigenome that is overexpressed in diverse carcinomas. We show here that MUC1-C represses RASSF1A expression in multiple types of KRAS wild-type and mutant cancer cells. Mechanistically, MUC1-C occupies the RASSF1A promoter in a complex with the ZEB1 transcriptional repressor. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123860/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510078
Series		Accession: GSE123860	ID: 200123860

569. Estrogen signaling is reprogrammed in breast tumorigenesis
(Submitter supplied) Limited knowledge of the changes in estrogen receptor (ER) signaling during the transformation of the normal mammary gland to breast cancer hinders the development of effective prevention and treatment strategies. Differences in estrogen signaling between normal human primary breast epithelial cells and primary breast tumors obtained immediately following surgical excision were explored. Transcriptional profiling of normal ER+ mature luminal mammary epithelial cells and ER+ breast tumors revealed significant difference in the response to estrogen stimulation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 107 Samples
FTP download: GEO (BROADPEAK, CSV, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99680/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389287
Series		Accession: GSE99680	ID: 200099680

570. The Wnt/β-catenin and RAS-ERK Pathways were Activated  in Tissues of Chemotherapy-Resistant Gastric Cancer PDX Tumor
(Submitter supplied) Chemotherapy resistance and disease recurrence remains major causes of gastric cancer patient mortality. We describe possible relationship between Wnt/b-catenin and RAS/ERK pathways in GC patients and acquired-resistant GC PDX tumors against FOLFOX, 5-fluorouracil-based chemotherapy. RNA sequencing analysis also demonstrates that Wnt/b-catenin pathway is an actionable target pathway for overcoming the chemotherapy resistance. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128967/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529583
Series		Accession: GSE128967	ID: 200128967

571. Next generation sequencing on knockdown of AC093323.3 in lung cancer cells
(Submitter supplied) In this study we predict functionally important long intergenic non-coding RNAs (lincRNAs) with a role in core essential processes in human. One of the candidate lincRNA, AC093323.3, was experimentally verified to affect cell viability. We performed RNASeq on knockdown of AC093323.3 to further investigate the functional role of this lincRNA.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115659/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475690
Series		Accession: GSE115659	ID: 200115659

572. Combined Targeting of Estrogen Receptor alpha and XPO1 prevent Akt activation, remodel metabolic pathways and induce autophagy to overcome tamoxifen resistance
(Submitter supplied) Majority of breast cancer specific deaths in women with ERα (+) tumor occur due to metastases that are resistant to endocrine therapy. There is a critical need for novel therapeutic approaches to resensitize recurrent ERα (+) tumors to endocrine therapies. The objective of this study was to elucidate mechanisms of improved effectiveness of combined targeting of ERα and XPO1, a nuclear transport protein in overcoming endocrine resistance. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112883/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA449383
Series		Accession: GSE112883	ID: 200112883

573. Transcriptomes of human trophoblast cell lines
(Submitter supplied) We report the transcriptomes of human choriocarcinoma cell lines JEG3 and BeWo in order to provide information about genes expressed by human trophoblasts.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131753/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA544683
Series		Accession: GSE131753	ID: 200131753

574. The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders [lnc-Nr2f1 overexpression]
(Submitter supplied) The goal is to examine the global transcriptomic changes upon lnc-Nr2f1 overexpression in human neuroblastoma cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125267/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515716
Series		Accession: GSE125267	ID: 200125267

575. Loss of histone macroH2A1 in hepatocellular carcinoma cells promotes paracrine-mediated chemoresistance and CD4+CD25+ T regulatory cells activation
(Submitter supplied) We recently described the phenotype of HepG2 and Huh-7, hepatocellular carcinoma cells, knocked down for histone variant macroH2A1. Both cell lines acquire a cancer stem cell phenotype (Lo Re O et al., Hepatology 2017, PMID: 28913935; Lo Re O et al., Epigenetics 2018, PMID: 30165787). We found that short hairpin RNA-mediated macroH2A1 knockdown induced acquisition of CSC-like features, including the growth of significantly larger and less differentiated tumors when injected into nude mice. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131680/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA544415
Series		Accession: GSE131680	ID: 200131680

576. Clonal replacement of tumor-specific T cells following PD-1 blockade
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
4 related Platforms 124 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123814/
Series		Accession: GSE123814	ID: 200123814

577. Clonal replacement of tumor-specific T cells following PD-1 blockade [single cells]
(Submitter supplied) Immunotherapies that block inhibitory checkpoint receptors on T cells have transformed the clinical care of cancer patients. However, the clonal origin of tumor-specific T cells following checkpoint blockade in patients remains unclear. Here, we performed paired single-cell RNA- and T cell receptor (TCR)- sequencing on site-matched tumors from patients with basal cell carcinoma (BCC) pre- and post-anti-PD-1 therapy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL15520 GPL20301 GPL18573 86 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123813/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509910
Series		Accession: GSE123813	ID: 200123813

578. Clonal replacement of tumor-specific T cells following PD-1 blockade [bulk RNA]
(Submitter supplied) Immunotherapies that block inhibitory checkpoint receptors on T cells have transformed the clinical care of cancer patients. However, the clonal origin of tumor-specific T cells following checkpoint blockade in patients remains unclear. Here, we performed paired single-cell RNA- and T cell receptor (TCR)- sequencing on site-matched tumors from patients with basal cell carcinoma (BCC) pre- and post-anti-PD-1 therapy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 38 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123812/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509911
Series		Accession: GSE123812	ID: 200123812

579. Allosteric Antagonist Modulation of TRPV2 by Piperlongumine Impairs Glioblastoma Progression
(Submitter supplied) Using machine learning to identify biological targets for natural products with anticancer properties and unknown modes of action is gaining momentum. Herein, we employ machine intelligence to deconvolute the phenotypic effects of the natural product Piperlongumine (PL) and establish an unprecedented link to allosteric modulation of the human transient receptor potential vanilloid 2 (hTRPV2) channel. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131660/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA544318
Series		Accession: GSE131660	ID: 200131660

580. RNA sequencing results of EMT and CSC phenotypes induced by modulated expression of wild-type and mutated PSPC1 and PTK6
(Submitter supplied) We found that PSPC1 is the master activator for transcription factors of EMT and stemness and accompanies c-Myc activation to facilitate tumour growth.  To elucidate mechanisms that the underlying post-translational modification of PSPC1, we performed the RNA-seq analysis of overexpression of PSPC1, alone and with PTK6, and PSPC1 tyrosine residue mutation in SK-Hep1 cells. We performed c-terminal of PSPC1 and its mutated nuclear localization site (NLS) in Mahlavu cells to evaluate its inhibitory effects on gene expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114856/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472874
Series		Accession: GSE114856	ID: 200114856

581. Linking aberrant chromatin features in chronic lymphocytic leukemia to deregulated transcription factor networks
(Submitter supplied) In chronic lymphocytic leukemia (CLL) a diverse set of genetic mutations is embedded in a deregulated epigenetic landscape that drives cancerogenesis. To elucidate the role of aberrant chromatin features, we mapped DNA methylation, 7 histone modifications, nucleosome positions, chromatin accessibility, binding of EBF1 and CTCF as well as the transcriptome of B cells from CLL patients and healthy donors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL20301 GPL11154 519 Samples
FTP download: GEO (BIGBED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113336/
Series		Accession: GSE113336	ID: 200113336

582. Radiation enhances melanoma response to immunotherapeutic and synergizes with benzodiazepines to promote improved anti-tumor activity
(Submitter supplied) The RNA-Seq data of 17 brain metastatic samples short-read sequences were aligned to the hg19 human reference genome using STAR (v 2.4.1a). featureCounts was used to count the reads of the mapped bam files. SAMseq was used to conduct differential expression analysis among the two treatment groups. SAMseq was utilized as it accounts for potential correlation in expression among genes and its permutation-based testing method was deemed more appropriate for a smaller sample size. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131521/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA543883
Series		Accession: GSE131521	ID: 200131521

583. Expression analysis of ethanol treatment on SK-N-BE(2)
(Submitter supplied) To evaluate the impact of ethanol treatment on neuronal cells, we examined the expression of SK-N-BE(2) neuronal cell line 24 h and 42 h after treating with 10 mM and 20 mM ethanol by RNA sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131470/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA543781
Series		Accession: GSE131470	ID: 200131470

584. O-GlcNAc transferase fine-tunes MYC-dependent transcription to promote cell cycle
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 36 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121474/
Series		Accession: GSE121474	ID: 200121474

585. O-GlcNAc transferase fine-tunes MYC-dependent transcription to promote cell cycle [RNA-seq]
(Submitter supplied) O-GlcNAc transferase (OGT) is overexpressed in aggressive prostate cancer. Here, we employed ChIP-seq to map chromatin-bound O-GlcNAc loci in prostate cancer cells and discovered that these overlap with sites of active transcription and MYC binding. Using RNA-seq, we show that inhibition of OGT promotes MYC-dependent transcriptional repression of mRNAs involved in G1-S transition. O-GlcNAc ChIP-seq regions are highly enriched to transcription start sites and identify the ‘GFY’-motif. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121472/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497432
Series		Accession: GSE121472	ID: 200121472

586. NCOA5 knockout suppresses epithelial-to-mesenchymal transition (EMT) impairing cell proliferation and migration in Hepatocellular Carcinoma cells
(Submitter supplied) Nuclear receptor coactivator 5 (NCOA5) is an AF2-independent coactivator that contains both transcriptional activation and repression domains. Previous studies have shown that NCOA5 plays an important role in the development of a variety of malignancies. However, the underlying mechanisms remain unclear. In our study, we successfully generated the NCOA5 knockout liver cancer cell lines by CRISPR/Cas9 -mediated genome editing and found that NCOA5 knockout inhibited the proliferation and migration of hepatocellular carcinoma (HCC) cells significantly, meanwhile led to a marked decrease in tumor microsphere formation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111829/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438307
Series		Accession: GSE111829	ID: 200111829

587. Organoids derived from directly reprogrammed human hepatocytes for modeling liver cancer initiation
(Submitter supplied) Hepatocellular carcinoma (HCC) and cholangiocarcinoma (ICC) are two main forms liver cancers with poor prognosis. Models for studying HCC and ICC development using human liver cells are urgently needed. Organoids serve as in vitro models for cancer studies as it recapitulates in vivo structures and microenvironment of solid tumors. Herein, we established liver cancer organoid models by introducing specific mutations into human induced hepatocyte (hiHep)-derived organoids. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115853/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476313
Series		Accession: GSE115853	ID: 200115853

588. Gene expression activation in CLL mediated by MSCs contact
(Submitter supplied) Survival of primary CLL cells is mediated by mesenchimal stromal cells in vitro. The goal of this study is to compare the gene expression profile of primary CLL cells in monoculture to that one following cell-cell contact with MSCs
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99724/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389433
Series		Accession: GSE99724	ID: 200099724

589. The effects of chemokines CCL2/7 on MDA-MB-231-FOXC1 cells
(Submitter supplied) Our preliminary studies performed in vitro show that MDA-MB-231-FOXC1 cell, which were used to mimic the lung-colonizing triple-negative breast cancer cells, was an indispensable component for the induction of migration and tube formation of lung endothelial cells. Moreover, our results further show that mouse lung fibroblast-derived chemokines CCL2/7 act on MDA-MB-231-FOXC1 cells, which mediates the migration and tube formation of lung endothelial cells in vitro. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131383/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA543438
Series		Accession: GSE131383	ID: 200131383

590. The X-linked DDX3X RNA helicase dictates translation re-programming and metastasis in melanoma
(Submitter supplied) The X-linked DDX3X gene encodes an ATP-dependent DEAD-box RNA helicase frequently altered in various human cancers including melanomas. Despite its important roles in translation and splicing, how DDX3X dysfunction specifically rewires gene expression in melanoma remains completely unknown. Here we uncover a DDX3X-driven post-transcriptional program that dictates melanoma phenotype and poor disease prognosis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131343/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA543304
Series		Accession: GSE131343	ID: 200131343

591. Drug combination of 17-AAG and Belinostat on MDA-MB-231 breast cancer cells
(Submitter supplied) Breast cancer is the most common cancer that threatens women's health. While the strategy of drug combination can help to reduce adverse effects and to overcome the resistance of clinical treatment of single drug. In this work, we report the synergetic effect between a HSP90 inhibitor 17-AAG and a HDAC inhibitor Belinostat, on the triple-negative breast cancer MDA-MB-231 cells. The RNA-Seq data analysis showed that the most over-represented KEGG pathways in the combination group came from migration or invasion related genes, which were not observed in the differentially expressed genes after the treatment of 17-AAG or Belinostat alone.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129944/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA533241
Series		Accession: GSE129944	ID: 200129944

592. Intrinsic Resistance to MEK Inhibition Through BET Protein Mediated Kinome
(Submitter supplied) Mutation or deletion of Neurofibromin (NF1), an inhibitor of RAS signaling, frequently occurs in epithelial ovarian cancer (EOC), supporting therapies that target downstream RAS effectors, such as the RAF-MEK-ERK pathway. However, no comprehensive studies have been carried out testing the efficacy of MEK inhibition in NF1-deficient EOC.  Here, we performed a detailed characterization of MEK inhibition in NF1-deficient EOC cell lines using kinome profiling and RNA sequencing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127886/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA525696
Series		Accession: GSE127886	ID: 200127886

593. Blocking expression of inhibitory receptor NKG2A overcomes tumor resistance to NK cells
(Submitter supplied) A key mechanism of tumor resistance to immune cells is mediated by expression of peptide-loaded HLA-E in tumor cells, which suppresses natural killer (NK) cell activity via ligation of the NK inhibitory receptor CD94/NKG2A. To bypass HLA-E inhibition, we developed a way to generate highly functional NK cells lacking NKG2A. Constructs containing a single-chain variable fragment derived from an anti-NKG2A antibody were linked to endoplasmic reticulum-retention domains. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127081/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA524164
Series		Accession: GSE127081	ID: 200127081

594. Transcriptome analysis in shNull and shSETD8 medulloblastoma cells
(Submitter supplied) The goal of this study was to determine the effect on gene transcription profiles in medulloblastoma cells that were depeleted of the epigenomic modifier SETD8 vs control.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121247/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA496472
Series		Accession: GSE121247	ID: 200121247

595. Analysis of copy number alterations from a lncRNA perspective reveals ALAL-1 a mediator of NSCLC immune evasion.
(Submitter supplied) Analysis of the transcriptomic changes after ALAL-1 knockdown in HCC95 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21697 12 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114632/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472029
Series		Accession: GSE114632	ID: 200114632

596. DEDD regulates cell cycle related genes
(Submitter supplied) In DEDD knocked-down triple-negative breast cancer, cell cycle related gene expressions have been altered
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131303/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA543152
Series		Accession: GSE131303	ID: 200131303

597. JAK/STAT inhibition in macrophages promotes therapeutic resistance by inducing expression of protumorigenic factors
(Submitter supplied) Tumor-associated macrophages contribute to tumor progression and therapeutic resistance in breast cancer. Within the tumor microenvironment, tumor-derived factors activate pathways that modulate macrophage function. Using in vitro and in vivo models, we find that tumor-derived factors induce activation of the Janus kinase (JAK)/signal transducer and activator of transcription 3 (STAT3) pathway in macrophages. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131300/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA543149
Series		Accession: GSE131300	ID: 200131300

598. RNA-seq of human aneuploid cell lines with Trisomy 21
(Submitter supplied) Trisomy 21, a form of aneuploidy, is one of the few viable forms of trisomy. The goal of this study was to assess the effect of an additional chromosome 21 on gene expression in two different human aneuploid model cell lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131249/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA543056
Series		Accession: GSE131249	ID: 200131249

599. Transcriptional control of subtype switching ensures adaptation and growth of pancreatic cancer
(Submitter supplied) Purpose: The goal of this study is to determine whether ectopic expression of the GLI2 transcription factor in the human pancreatic cancer cell line, YAPC is sufficient to cause gene expression changes associated with a EMT switch. Methods: RNA was isolated from YAPC cells engineered to express a doxycycline inducible cassette for ectopic expression of GLI2 following treatment with 1ug/ml of Dox for 6 days. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131222/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA543003
Series		Accession: GSE131222	ID: 200131222

600. RNA-seq analyses of human prostate cancer cells
(Submitter supplied) To study the transcriptome of human prostate cancer cells, RNA-seq experiments were performed.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128201/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA526724
Series		Accession: GSE128201	ID: 200128201

601. Apatinib preferentially inhibits Gefitinib-resistant lung cancer cells by inducing cell cycle arrest and inhibiting VEGFR signaling pathway
(Submitter supplied) Targeted therapy for patients with EGFR mutations by tyrosine kinase inhibitors (TKIs) has provided a significant benefit to patients. However, gradually developed resistance to the therapy becomes a major challenge in clinical practice. Herein, we report that Apatinib, an anti-angiogenic drug, strongly and specifically inhibits Gefitinib-resistant cancer cells but not their parental sensitive cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129221/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA530546
Series		Accession: GSE129221	ID: 200129221

602. SREBP1 drives Keratin 80-dependent cytoskeletal changes and invasive behavior in endocrine resistant ERα breast cancer
(Submitter supplied) Approximately 30% of women diagnosed with ERα breast cancer relapse with metastatic disease following adjuvant treatment with endocrine therapies. The connection between acquisition of drug resistance and invasive potential is poorly understood. In this study, we demonstrate that the type II keratin topological associating domain (TAD) undergoes epigenetic reprogramming in cells that develop resistance to aromatase inhibitors (AI), leading to keratin 80 (KRT80) upregulation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125128/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515297
Series		Accession: GSE125128	ID: 200125128

603. Global RNA expression profiles between shNC and shcircβ-catenin in PLC/PRF/5 cells
(Submitter supplied) Circular RNAs are a class of non-coding RNA transcripts, which are ubiquitously expressed in eukaryotes. In the current study, we identified a novel circRNA derived from β-catenin gene locus, which was named “circβ-catenin”. In order to characterize the function of circβ-catenin in modulating Wnt pathway, we conducted RNA-seq to evaluate the effect of circβ-catenin on global RNA expression profiles.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124527/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512375
Series		Accession: GSE124527	ID: 200124527

604. Clonal evolution patterns in acute myeloid leukemia with NPM1 mutation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome variation profiling by SNP array
Platforms: GPL6801 GPL11154 92 Samples
FTP download: GEO (CEL, CHP) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128604/
Series		Accession: GSE128604	ID: 200128604

605. Clonal evolution patterns in acute myeloid leukemia with NPM1 mutation (RNA-seq data set)
(Submitter supplied) Mutations in the nucleophosmin 1 (NPM1) gene are considered founder mutations in the pathogenesis of acute myeloid leukemia (AML). To further characterize the genetic composition of NPM1 mutated (NPM1mut) AML, we assess mutation status of five recurrently mutated oncogenes (FLT3, DNMT3A, IDH1, IDH2, NRAS) in 129 paired NPM1mut samples obtained at diagnosis and relapse. We find a substantial shift in the genetic pattern from diagnosis to relapse including NPM1mut loss (n=11). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128603/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA528269
Series		Accession: GSE128603	ID: 200128603

606. Tumor suppressor SMARCB1 suppresses super-enhancers to govern hESC lineage determination
(Submitter supplied) The SWI/SNF complex is a critical regulator of pluripotency in human embryonic stem cells (hESCs), and individual subunits have varied and specific roles during development and in diseases. The core subunit SMARCB1 is required for early embryonic survival, and mutations can give rise to atypical teratoid/rhabdoid tumors (AT/RTs) in the pediatric central nervous system. We report that in contrast to other studied systems, SMARCB1 KD relieves bivalent gene repression in hESCs and promotes chromatin accessibility at super-enhancers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL18573 30 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128351/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA527217
Series		Accession: GSE128351	ID: 200128351

607. Acute deletion of CTCF disrupted enhancer-promoter regulation of MYC in human cancer cells
(Submitter supplied) Myc is a family of regulator genes and proto-oncogenes that code for transcription factors. Gene expression of CTCF in human cancer cells and control uncover the disrupted enhancer-promoter regulation of MYC in human cancer cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 19 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120781/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494510
Series		Accession: GSE120781	ID: 200120781

608. Molecular mechanism impacted by circadian disruption underscores the importance of timed anti-cancer treatment
(Submitter supplied) Circadian disruption has multiple pathological consequences, but the underlying mechanisms are largely unclear. To address such mechanisms, we subjected cultured cells to chronic circadian desynchrony (CCD), mimicking a chronic jet-lag paradigm, and assayed a range of cellular functions.  The results indicated a specific circadian clock-dependent increase in cell proliferation. Transcriptome analysis revealed upregulation of G1-S-phase transition genes (cMyc, CyclinD1/3, Cdt1), concomitant with increased phosphorylation of the Retinoblastoma protein (Rb) by Cyclin D kinase 4/6 (CDK4/6) and increased G1-S progression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119668/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489887
Series		Accession: GSE119668	ID: 200119668

609. Cell cycle plasticity driven by MTOR signaling: integral mechanism for resistance to CDK4/6 inhibition
(Submitter supplied) Pancreatic ductal adenocarcinoma (PDAC), like many KRAS-driven tumors, preferentially loses CDKN2A to bypass the RB tumor suppressive pathway.   This finding and a gene expression profile indicative of a CDK4/6-driven cell cycle suggests that PDAC could be particularly sensitive to CDK4/6 inhibition.   Analysis of a panel of patient-derived cell lines and xenografts indicates that many pancreatic cancers have an intrinsic resistance to CDK4/6 inhibition that is not due to known molecular mechanisms. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 90 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113922/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454470
Series		Accession: GSE113922	ID: 200113922

610. RNASeq analysis of NB1691 neuroblastoma cells treated with MDM2-p53 inhibitor RG7388 alone and in combination with temozolomide
(Submitter supplied) To further identify potential mechanisms involved in combining RG7388 with temozolomide, GSEA was performed and revealed that RG7388 and temozolomide act cooperatively to upregulate the p53 pathway and downregulate MYC targets, the former resulting in significantly greater induction of several apoptotic genes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104917/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414128
Series		Accession: GSE104917	ID: 200104917

611. Biomarkers of Cavernous Angioma with Symptomatic Hemorrhage (CASH)
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL20301 25 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130176/
Series		Accession: GSE130176	ID: 200130176

612. Biomarkers of Cavernous Angioma with Symptomatic Hemorrhage (CASH) [RNA-seq]
(Submitter supplied) Background: Cerebral cavernous angiomas with a symptomatic hemorrhage (CASH) have a high-risk of recurrent hemorrhage and serious morbidity. Methods: Eighteen plasma molecules with postulated mechanistic roles in cavernous angioma (CA) pathobiology were investigated in 114 patients and 12 healthy subjects. The diagnostic biomarker of a CASH in the prior year was derived as minimizing the Akaike Information Criterion (AIC) and validated using machine-learning, and then compared to the prognostic CASH biomarker predicting bleeding in the subsequent year. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130174/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA534219
Series		Accession: GSE130174	ID: 200130174

613. Pervasive H3K27 acetylation leads to ERV expression and a therapeutic vulnerability in H3K27M gliomas
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms 210 Samples
FTP download: GEO (BED, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128745/
Series		Accession: GSE128745	ID: 200128745

614. Total RNA-Seq data from leukemic patients with complex structural variants
(Submitter supplied) Structural variants can lead to an alteration of gene expression which may be associated with disease worsening. In our study we attempted to describe expression changes associated with the presence of extensive genomic rearrangements in chronic lymphocytic leukemia.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128668/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA528460
Series		Accession: GSE128668	ID: 200128668

615. Transcriptomes distinguish human FCD subtypes
(Submitter supplied) Focal Cortical Dysplasia (FCD) is a major cause of drug-resistant focal epilepsy in children and the clinico-pathological classification remains a challenging issue in daily practice. With the recent progress in DNA methylation based classification of human brain tumors we examined, whether genomic DNA methylation and gene expression analysis can be used to also distinguish human FCD subtype
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 28 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128300/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA527060
Series		Accession: GSE128300	ID: 200128300

616. Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia (RNA-seq of KLF6 KO)
(Submitter supplied) Aging is associated with functional decline of hematopoietic stem cells (HSC) as well as an increased risk of myeloid malignancies. We performed an integrative characterization of epigenomic and transcriptomic changes, including single-cell RNA-seq, during normal human aging. Lineage-CD34+CD38- cells (HSC-enriched, HSCe) undergo age-associated epigenetic reprogramming consisting of redistribution of DNA methylation and reductions in H3K27ac, H3K4me1 and H3K4me3. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121560/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497796
Series		Accession: GSE121560	ID: 200121560

617. Pervasive H3K27 acetylation leads to ERV expression and a therapeutic vulnerability in H3K27M gliomas [RNA-Seq]
(Submitter supplied) Epigenetic alterations are recurrently observed in cancer and are the subject of active therapeutic investigations. Midline high-grade gliomas (HGGs) are deadly brain tumors characterized by lysine-to-methionine substitutions at position 27 in histone 3 (H3) variants (denoted H3K27M), which are core components of the nucleosome. H3K27M, the first event in midline HGG development, results in a drastic loss of the repressive histone mark H3K27 tri-methylation (H3K27me3), and a notable increase in H3K27 acetylation (H3K27ac), a mark associated with active chromatin and cellular identity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL16791 GPL20301 GPL11154 96 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117446/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482128
Series		Accession: GSE117446	ID: 200117446

618. Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia (RNA-Seq of LMNA KD)
(Submitter supplied) Aging is associated with functional decline of hematopoietic stem cells (HSC) as well as an increased risk of myeloid malignancies. We performed an integrative characterization of epigenomic and transcriptomic changes, including single-cell RNA-seq, during normal human aging. Lineage-CD34+CD38- cells (HSC-enriched, HSCe) undergo age-associated epigenetic reprogramming consisting of redistribution of DNA methylation and reductions in H3K27ac, H3K4me1 and H3K4me3. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116254/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA477864
Series		Accession: GSE116254	ID: 200116254

619. Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL21290 GPL16791 139 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104408/
Series		Accession: GSE104408	ID: 200104408

620. Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia (RNA-Seq of HSCe)
(Submitter supplied) Aging is associated with functional decline of hematopoietic stem cells (HSC) as well as an increased risk of myeloid malignancies. We performed an integrative characterization of epigenomic and transcriptomic changes, including single-cell RNA-seq, during normal human aging. Lineage-CD34+CD38- cells (HSC-enriched, HSCe) undergo age-associated epigenetic reprogramming consisting of redistribution of DNA methylation and reductions in H3K27ac, H3K4me1 and H3K4me3. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104406/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA412570
Series		Accession: GSE104406	ID: 200104406

621. Transcription factor NKX3-1 is required for reprogramming to pluripotency and can replace OCT4 in mouse and human iPSC induction [RNA-seq]
(Submitter supplied) Resolution of early molecular events preceding endogenous OCT4 activation is critical to understanding the mechanism of reprogramming somatic cells to induced pluripotent stem cells (iPSCs), yet capturing transient regulators at the onset of reprogramming is difficult in heterogeneous populations of asynchronously reprogramming fibroblasts following four-factor transduction. To address this need, we used a heterokaryon system to identify an early and transiently expressed homeobox transcription factor, NKX3-1. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
4 related Platforms 25 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103509/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401768
Series		Accession: GSE103509	ID: 200103509

622. Group 3 innate lymphoid cells mediate early protective immunity against Mycobacterium tuberculosis
(Submitter supplied) We report the phenotype of human lung ILC2 and ILC3 populations from individuals with tuberculosis (TB) and non-TB cancer controls. We find that ILC2s demonstrate moderate transcriptional differences in TB infection, whereas ILC3s demonstrate large differences.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131031/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA542348
Series		Accession: GSE131031	ID: 200131031

623. Estrogen receptor and mTOR signaling rewires cancer metabolism in obesity-associated breast cancer
(Submitter supplied) Obesity is a risk factor for postmenopausal ERα (+) breast cancer. Molecular mechanisms activated by the factors from serum that contribute to this risk and how these mechanisms affect ERα signaling are yet to be elucidated. To identify such mechanisms, we performed whole metabolite and protein profiling in serum samples, which enabled us to focus on factors that were differentially present in serum from cancer-free vs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL16791 21 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114372/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471101
Series		Accession: GSE114372	ID: 200114372

624. Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia
(Submitter supplied) Aging is associated with functional decline of hematopoietic stem cells (HSC) as well as an increased risk of myeloid malignancies. We performed an integrative characterization of epigenomic and transcriptomic changes, including single-cell RNA-seq, during normal human aging. Lineage-CD34+CD38- cells (HSC-enriched, HSCe) undergo age-associated epigenetic reprogramming consisting of redistribution of DNA methylation and reductions in H3K27ac, H3K4me1 and H3K4me3. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 650 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104379/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA412479
Series		Accession: GSE104379	ID: 200104379

625. Single-cell lymphocyte heterogeneity inadvanced Cutaneous T-Cell Lymphoma skin tumors
(Submitter supplied) Purpose: The heterogeneity of tumor cells presents a major challenge to cancer diagnosis and therapy. Cutaneous T cell lymphomas (CTCL) are a group of T lymphocyte malignanciesthat primarily affect skin. Lack of highly specific markers for malignant lymphocytes prevents early diagnosis, while only limited treatment options are available for patients with advanced-stage CTCL.Droplet-basedsingle-cell transcriptome analysis of CTCL skin biopsiesopens avenues for dissecting patient-specificT lymphocyte heterogeneity, providing a basis for identifying specific markers for diagnosis and cure of CTCL. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128531/
Series		Accession: GSE128531	ID: 200128531

626. RNA sequencing results of wild type and overexpresssion or knockdown PTTG3P in LUAD cell lines based on IlluminaNovaSeq 6000 platform
(Submitter supplied) We found that PTTG3P expression perturbed cancer cell proliferation in lung adenomacarcinoma.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114826/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472773
Series		Accession: GSE114826	ID: 200114826

627. MeRIP-seq for heat shock in B-cell lymphoma cells
(Submitter supplied) We ran MeRIP-seq on RNA from heat shocked (43 C for 1 hr) and untreated cells to compare to previous reports as part of an evaluation of MeRIP-seq reproducibility.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 12 Samples
FTP download: GEO (NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130892/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA541915
Series		Accession: GSE130892	ID: 200130892

628. The chromatic loci of H3.3K36M determine the preferential prevalence of K36M mutation at H3.3 in chondroblastomas
(Submitter supplied) The histone H3.3K36M mutation, identified in over 90% of chondroblastoma cases, reprograms the H3K36 methylation landscape and gene expression to promote tumorigenesis. However, it’s still unknown how the H3K36M mutation preferentially happens at the histone H3 variant H3.3. Here we report that, H3.3K36M mutation, but not H3.1K36M mutation, promoted increased colony formation and defects in differentiation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL23227 GPL20795 52 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130858/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA541831
Series		Accession: GSE130858	ID: 200130858

629. Identification of SERPINE1 as a Regulator of Glioblastoma Cell Dispersal via Analyzing Dynamic Transcriptome of Dispersing Cells
(Submitter supplied) With a model mimicking GBM tumor cell dispersal, transcriptome changes between core (immotile) and dispersive (motile) cells were analyzed. Many genes are differentially expressed between these populations. This study focused on the genes that are significantly upregulated in dispersive cells. Besides gene sets related with the cell cycle and cell survival, epithelial to mesenchymal transition gene set is upregulated in dispersive cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130857/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA541828
Series		Accession: GSE130857	ID: 200130857

630. MCF-7 as a model for functional analysis of breast cancer risk variants
(Submitter supplied) Here we report how the ER+ cell line MCF-7 can be used to inform risk mechanisms for BCa. We identified active regulatory elements (enhancers, promoters, and chromatin organizing elements) by histone H3K27 acetylation and CTCF occupancy and determined the enrichment of risk variants at these sites. We measured gene expression via RNA-seq. After intersection with GWAS risk variants we found 39 enhancers and 15 CTCF occupancy sites that, between them, overlapped 96 BCa credible risk variants at 42 loci. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (BED, BW, TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130852/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA541872
Series		Accession: GSE130852	ID: 200130852

631. RNA-Seq of PRMT1 overexpression ECA109 cells
(Submitter supplied) RNA-seq was performed on three biological replicates. Total RNA from ECA109 LV-GFP/LV-PRMT1.Differentially expressed genes were considered to be significant between groups when the P-value was <0.05 and the fold change of expression was ≥2-fold or ≤0.5-fold.  By this way, the RNA-Seq data showed the differential expression genes in PRMT1 overexpression ECA109 cells compared with NC cells. Furthermore, Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of the differentially expressed genes in the experiment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128913/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529370
Series		Accession: GSE128913	ID: 200128913

632. KLF4 as a rheostat of osteolysis and osteogenesis in prostate tumors in the bone
(Submitter supplied) We previously found that KLF4, a gene highly expressed in adult prostate stem cells, blocks the progression of indolent intraepithelial prostatic lesions into aggressive and rapidly growing tumors. To test whether this anti-cancer effect of KLF4 can also prevent prostate cancer-induced damage to the bone, we ablated KLF4 in human PC3 prostate cancer cells using CRISPR/Cas9-mediated genome editing and compared their behavior to null cells transduced with a DOX inducible KLF4 expression system. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117965/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483806
Series		Accession: GSE117965	ID: 200117965

633. Effect of Ro 08-2750 treatment on gene expression of human leukemia cell lines MOLM13 and K562
(Submitter supplied) RNA-sequencing on human leukemia cell lines MOLM13 (AML, MLL-AF9+) and K562 (CML-BC, BCR-ABL+) after Ro 08-2750 treatment (20 uM, 4hours)
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114320/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA470944
Series		Accession: GSE114320	ID: 200114320

634. Aberrant expression of select piRNA-pathway genes does not reactivate piRNA silencing in cancer cells
(Submitter supplied) Analysis of PIWIL1 function in COLO205 [ATCC® CCL-222] colon adenocarcinoma cancer cell culture model. 
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL16791 GPL21290 GPL11154 32 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128526/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA528177
Series		Accession: GSE128526	ID: 200128526

635. Highly-motile versus unsorted MDA-MB-231 breast cancer cells
(Submitter supplied) The challenge of predicting which patients with breast cancer will develop metastases leads to the overtreatment of patients with benign disease and to the inadequate treatment of the aggressive cancers. Here, we report the development and testing of a microfluidic assay that quantifies the abundance and proliferation of migratory cells in breast-cancer specimens, for the assessment of their metastatic propensity and for the rapid screening of potential antimetastatic therapeutics. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128313/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA527110
Series		Accession: GSE128313	ID: 200128313

636. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [AmpliSeq]
(Submitter supplied) Background: High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades since the first mRNA profiling microarrays. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it difficult to directly evaluate performance, reliability and to what extent gene expression data from different platforms can be compared or integrated. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130762/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA541297
Series		Accession: GSE130762	ID: 200130762

637. High-throughput tissue dissection and cell purification with digital cytometry [healthy adults]
(Submitter supplied) Tissue composition is a major determinant of phenotypic variation and a key factor influencing disease outcomes. Although scRNA-Seq has emerged as a powerful technique for characterizing cellular heterogeneity, it is currently impractical for large sample cohorts and cannot be applied to fixed specimens collected as part of routine clinical care. To overcome these challenges, we extended Cell type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) into a new platform for in silico cytometry. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127813/
Series		Accession: GSE127813	ID: 200127813

638. High-throughput tissue dissection and cell purification with digital cytometry
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL570 GPL20301 GPL18573 315 Samples
FTP download: GEO (CEL, MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127472/
Series		Accession: GSE127472	ID: 200127472

639. High-throughput tissue dissection and cell purification with digital cytometry [scRNA-Seq]
(Submitter supplied) Tissue composition is a major determinant of phenotypic variation and a key factor influencing disease outcomes. Although scRNA-Seq has emerged as a powerful technique for characterizing cellular heterogeneity, it is currently impractical for large sample cohorts and cannot be applied to fixed specimens collected as part of routine clinical care. To overcome these challenges, we extended Cell type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) into a new platform for in silico cytometry. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 1 Sample
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127471/
Series		Accession: GSE127471	ID: 200127471

640. RNAseq transcriptomic profile of glioblastoma stem-like cells derived from U87MG cell line treated with a selective A3 adenosine receptor antagonist (MRS1220) under hypoxia
(Submitter supplied) Glioblastoma Multiforme (GBM) is the primary brain tumor with the highest incident and mortality rates worldwide. This is because therapies are not effective, mainly due to tumor recurrence after surgical resection and chemotherapeutic treatment. Recurrence is mainly produced by a tumoral cell sub-population called Glioblastoma Stem-like Cells (GSCs), which are primarily responsible for chemo-resistance and tumor infiltration. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT, XLS, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100146/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA390853
Series		Accession: GSE100146	ID: 200100146

641. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [RNA-Seq]
(Submitter supplied) Background: High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades since the first mRNA profiling microarrays. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it difficult to directly evaluate performance, reliability and to what extent gene expression data from different platforms can be compared or integrated. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130660/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540926
Series		Accession: GSE130660	ID: 200130660

642. RNA-seq and m6A-seq of AML cells with FTO knockdown or inhibition
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other; Methylation profiling by high throughput sequencing
Platforms: GPL16791 GPL15433 16 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103497/
Series		Accession: GSE103497	ID: 200103497

643. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
7 related Platforms 121 Samples
FTP download: GEO (CEL, IDAT, RCC) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130645/
Series		Accession: GSE130645	ID: 200130645

644. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [QiaSeq]
(Submitter supplied) Background: High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades since the first mRNA profiling microarrays. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it difficult to directly evaluate performance, reliability and to what extent gene expression data from different platforms can be compared or integrated. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21697 25 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130644/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540861
Series		Accession: GSE130644	ID: 200130644

645. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [BioSpyder_TempoSeq]
(Submitter supplied) Background: High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades since the first mRNA profiling microarrays. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it difficult to directly evaluate performance, reliability and to what extent gene expression data from different platforms can be compared or integrated. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21697 25 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130643/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540856
Series		Accession: GSE130643	ID: 200130643

646. mRNA expression profiling in MDA-MB-231 (LM1) cells with a tet-incible MBD2 or p66α knock down, or treated with MBD2-targeting small molecule ABA or APC
(Submitter supplied) The goal of this study is to compare mRNA expression profiles among wild type, MBD2 knock down, p66α knock down, and ABA- and APC-treated cells.. All cell lines were maintained in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. For the doxycycline inducible gene expression regulation, each cell lines were incubated in the presence of 1 μg/ml doxycycline for 2 days. For the drug treatment, MDA-MB-231 (LM1) cells were incubated in the presence of 10 μM ABA or APC for 2 days. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130637/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540857
Series		Accession: GSE130637	ID: 200130637

647. KRASG12C inhibition produces a driver-limited state revealing collateral dependencies
(Submitter supplied) Inhibitors targeting KRASG12C, a mutant form of the guanosine triphosphatase (GTPase) KRAS, are a promising new class of oncogene-specific therapeutics for the treatment of tumors driven by the mutant protein. These molecules react with the mutant cysteine residue by binding covalently to the switch-II pocket (S-IIP) that is present only in the inactive guanosine diphosphate (GDP)-bound state of KRASG12C, sparing the wild-type protein. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130616/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540780
Series		Accession: GSE130616	ID: 200130616

648. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [Lexogen_QuantSeq]
(Submitter supplied) Background: High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades since the first mRNA profiling microarrays. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it difficult to directly evaluate performance, reliability and to what extent gene expression data from different platforms can be compared or integrated. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21697 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130469/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540865
Series		Accession: GSE130469	ID: 200130469

649. RNA proximity sequencing reveals properties of spatial transcriptome organization in the nucleus
(Submitter supplied) Spatial transcriptomics aims to understand how the ensemble of RNA molecules in tissues and cells is organized in 3D space. Here we introduce Proximity RNA-seq, which identifies co-localization preferences for pairs or groups of chromatin-associated, nuclear-retained and nascent RNAs in cell nuclei. Proximity RNA-seq is based on massive-throughput RNA barcoding of sub-nuclear particles in water-in-oil emulsion droplets, followed by sequencing.
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129732/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA532610
Series		Accession: GSE129732	ID: 200129732

650. PR attentuation of interferon signaling
(Submitter supplied) Why some tumors remain indolent and others progress to clinical relevance remains a major unanswered question in cancer biology. Interferon signaling in nascent tumors, mediated by STAT1, is a critical step through which the surveilling immune system can recognize and destroy developing tumors. Herein, we have identified an interaction between the progesterone receptor (PR) and STAT1 in breast cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126517/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA522252
Series		Accession: GSE126517	ID: 200126517

651. Targeting mitochondrial structure sensitizes AML to Venetoclax
(Submitter supplied) The BCL-2 family plays important roles in acute myeloid leukemia (AML) and Venetoclax, a selective BCL-2 inhibitor, has received FDA approval for treatment of AML. However, drug resistance ensues after prolonged treatment, highlighting the need for a greater understanding of the underlying mechanisms.  Using a genome-wide CRISPR/Cas9 screen in human AML, we identified genes whose inactivation sensitizes AML blasts to Venetoclax. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 26 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125403/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516226
Series		Accession: GSE125403	ID: 200125403

652. RPL12/uL11 phosphorylation regulates translation during mitosis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL17021 GPL11154 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112187/
Series		Accession: GSE112187	ID: 200112187

653. Therapeutic targeting of KDM1A/LSD1 in Ewing sarcoma engages the ER-stress response
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 44 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98787/
Series		Accession: GSE98787	ID: 200098787

654. Therapeutic targeting of KDM1A/LSD1 in Ewing sarcoma engages the ER-stress response II
(Submitter supplied) The transcriptional profile of LSD1 knockdown in A673 Ewing sarcoma cells mirrors that of EWS/FLI knockdown and LSD1 small molecule inhibition (SP-2509)
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98786/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA386199
Series		Accession: GSE98786	ID: 200098786

655. Therapeutic targeting of KDM1A/LSD1 in Ewing sarcoma engages the ER-stress response I
(Submitter supplied) The purpose of this study was to define biomarkers of  sensitivty and mechanisms of resistance to the KDM1A/LSD1 inhibtor SP-2509 (HCI-2509) in Ewing sarcoma cell lines. We report that regardless of drug sensitivity all cell lines engage the UPR and ER-stress response following treatment with SP-2509 resulting in apoptotic cytotoxicity. In addition hypersentsitive cell lines shared a common basal transcriptnomic profile, with hypersensitive cell lines signficantly inducing ETS1  which was not observed in sensitive cell  lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 36 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98785/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA386200
Series		Accession: GSE98785	ID: 200098785

656. Two dimensional and extracellular matrix based three-dimensional cultures of lung and breast cancer cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (COV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130591/
Series		Accession: GSE130591	ID: 200130591

657. Gene expression profiling in two dimensional and extracellular matrix based three-dimensional cultures of lung and breast cancer cells
(Submitter supplied) A549 and MDA-MB-231 cells were cultured in 2D and Matrigel based 3D culture for 4 days. Total RNA was extracted using Trizol. RNA-SEQ was carried out to profile the gene expression in both culture conditions.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130590/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540695
Series		Accession: GSE130590	ID: 200130590

658. Overexpression of poly(rC) binding protein 2 by alternative cleavage and polyadenylation promotes breast cancer progression via regulating UFD1 and NT5E
(Submitter supplied) Alternative cleavage and polyadenylation (APA) is an important post-transcriptional regulatory mechanism, which could lead many diseases. PCBP2 plays critical roles in mRNA stabilization, translational enhancement and contributes to human cancer development and progression even though the molecular mechanism is not completely understood. Herein, we report that increased expression of PCBP2 is observed in human breast cancer tissues compared to benign or normal breast tissues, and high expression of PCBP2 is significantly associated with disease progression and poor outcome in patients with breast cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130564/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540620
Series		Accession: GSE130564	ID: 200130564

659. Inactivation of CFTR by CRISPR/Cas9 alters transcriptional regulation of inflammatory pathways and other networks
(Submitter supplied) Individuals with cystic fibrosis (CF) experience elevated inflammation in multiple organs, but whether this reflects an inherent feature of CF cells or is a consequence of a pro-inflammatory environment is not clear. Using CRISPR/Cas9-mediated mutagenesis of CFTR, 17 subclonal cell lines were generated from Caco-2 cells.  Clonal lines with functional CFTR (CFTR+) were compared to those without (CFTR-) to directly address the role of CFTR in inflammatory gene regulation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL21697 GPL16791 24 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130226/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA534327
Series		Accession: GSE130226	ID: 200130226

660. Genome-wde mapping of BRD9 binding sites and gene expression changes upon BRD9 knockdown
(Submitter supplied) Leukemia is characterized by genetic and epigenetic mutations resulting in selection of cancer cells, which are unable to differentiate. While genetic alterations are difficult to target, the epigenome is intrinsically dynamic and readily offers new therapeutic strategies. Thus, identifying cancer-specific context-dependent targets and unraveling their biological function may open up new therapeutic perspectives. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129437/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA531322
Series		Accession: GSE129437	ID: 200129437

661. Estrogen receptor beta enhances chemotherapy response of GBM cells by down regulating DNA damage response pathways
(Submitter supplied) We examined the transcriptional changes modulated by estrogen receptor beta (ERβ) by performing global transcriptome analysis. U87 cells were transduced with lentiviral particles carrying either empty vector or ERβ-FLAG expression vector and the RNA was isolated and utilized for RNA-seq analysis. Our results demonstrated that ERβ modulated genes were related to homologous recombination, DNA damage response, ATM signaling and cell cycle pathways.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121332/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497078
Series		Accession: GSE121332	ID: 200121332

662. Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in chronic lymphocytic leukemia
(Submitter supplied) Cancer evolution is fueled by genetic and epigenetic diversity, and intra-tumoral heterogeneity in DNA methylation has been shown to co-operate with genetic heterogeneity to empower evolutionary capacity of cancers such as chronic lymphocytic leukemia. Here, we show that epigenetic diversification leads to decreased coordination across layers of epigenetic information, likely reflecting an admixture of cells with diverging epigenetic identities. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 90 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119103/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488107
Series		Accession: GSE119103	ID: 200119103

663. Epigenetic evolution and lineage histories of chronic lymphocytic leukemia
(Submitter supplied) Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary course of cancer. In addition to genetic mutations, chronic lymphocytic leukemia (CLL) undergoes diversification through stochastic DNA methylation changes – epimutations. To measure the epimutation rate at single-cell resolution, we applied multiplexed reduced representation bisulfite sequencing (MscRRBS) to healthy donors B cells and CLL patient samples. more...
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 843 Samples
FTP download: GEO (CSV, TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109085/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA429620
Series		Accession: GSE109085	ID: 200109085

664. Transcriptome of locally advanced colorectal tumours
(Submitter supplied) Here, we report the genomic-scale characterization of locally advanced colon cancer transcriptome. Paraffin embedded samples was used to asses differences between normal colon, primary colon tumor an lymph node metastasis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 23 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100243/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391148
Series		Accession: GSE100243	ID: 200100243

665. Chromatin-informed inference of transcriptional programs in gynecologic cancers
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 30 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129339/
Series		Accession: GSE129339	ID: 200129339

666. Chromatin-informed inference of transcriptional programs in gynecologic cancers [RNA-Seq]
(Submitter supplied) RNA-seq of MDA-MB-436 cells  in control cells (shRen) and upon knockdown of MITF ( shQa, sh962) were generated by deep sequencing in duplicates
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129337/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA530973
Series		Accession: GSE129337	ID: 200129337

667. scRNA sequencing of 2 leukemia patients in remission after T cell therapy
(Submitter supplied) peripheral blood samples of two leukemia patients in remission were profiled by single cell RNA sequencing approximately 1 year after receiving WT1 specific transgenic T cell therapy, at a time when patients were in clinical remission
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128933/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529403
Series		Accession: GSE128933	ID: 200128933

668. Single cell RNAseq of human TCRVdelta 1 and TCRVdelta 2 gammadelta T lymphocytes purified from healthy adults blood
(Submitter supplied) γδ T lymphocytes represent ~1% of human PBMC and even more cells in most tissues of vertebrates. Although they have important anticancer functions, most current scRNA-Seq studies do not identify γδ T lymphocytes since their transcriptomes at the single cell level are unknown. Here we show that high resolution clustering of large scRNA-Seq data sets and a combination of gene signatures allow the specific detection of human γδ T lymphocytes and identification of their TCRVδ1 and TCRVδ2 subsets in large data sets from complex cell mixtures. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL21697 GPL21290 6 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128223/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA526841
Series		Accession: GSE128223	ID: 200128223

669. Heterogeneity and evolution in acute myeloid leukemia initiating cells
(Submitter supplied) Little is currently known about the heterogeneity of leukemic initiating cells and how they evolve during AML disease progression. AML exhibits extremely few DNA mutations (an average of 13 per patient); therefore, it is likely that RNA based changes also play crucial roles in the development and progression of AML. We have optimized a method to robustly and cost-effectively perform single cell RNA sequencing on AML initiating cells (CD34+CD38-CD45RA+CD90-Lin-7AAD-). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 813 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126068/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA520913
Series		Accession: GSE126068	ID: 200126068

670. Runx1 and Runx3 cooperatively repress Pmp22 to drive neurofibromagenesis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL17021 GPL570 17 Samples
FTP download: GEO (CEL, TDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122777/
Series		Accession: GSE122777	ID: 200122777

671. Chromosomal deletion and chromatin remodeling Drive ABT-199 Resistance in B-cell Lymphomas
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 73 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116132/
Series		Accession: GSE116132	ID: 200116132

672. Chromosomal deletion and chromatin remodeling Drive ABT-199 Resistance in B-cell Lymphomas [RNA-seq]
(Submitter supplied) Drug-tolerant “persister” cells underlie the emergence of drug-resistant clones and allow residual tumors to survive therapy; thus, represent an attractive therapeutic target to mitigate relapse.  With the promising outcome, yet some resistance cases surfaced after the approval of venetoclax (ABT-199), we defined a novel invasive drug resistance mechanism induced by Bcl2 inhibitor via examining the evolution of drug tolerant persister clones generated with ABT-199 treatment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 35 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116129/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA477352
Series		Accession: GSE116129	ID: 200116129

673. FRY Impacts Breast Cancer Malignancy by Inducing an Enrichment of Genes with Tumor-Suppressive Functions and Affecting EMT Potential of Breast Cancer Cells
(Submitter supplied) Breast cancer is a disease with diverse phenotypes, and while the progression of breast cancer from a localized lesion to metastatic disease is well understood clinically. Our previous study genetically linked the FRY gene with differential susceptibility to mammary carcinogenesis; however, little is known about the mechanistic insights of FRY in mammalian cells and breast cancer progression. Through RNA-Seq analysis of series of constructed cell lines based on highly malignant triple-negative human breast cancer cells MDA-MB-231, we show that enhanced FRY induces massive changes in gene expression, which favor signalings and molecules with tumor-suppressive functions and engage in promoting cell differentiation, maintaining the normal and histopathological characteristics of epithelial cells, and in regulating EMT potential of breast cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112910/
Series		Accession: GSE112910	ID: 200112910

674. A phosphoproteomic and transcriptomic analysis of carnosine’s action on signaling in glioblastoma
(Submitter supplied) Previous studies demonstrated that carnosine affects signaling molecules of different pathways in a number of experimental models. However, the primary targets of carnosine are still unknown and its effect on complex signal transduction has not been revealed. This is especially the case for pathways that could be responsible for the anti-neoplastic effect of the dipeptide. Therefore, we performed a phosphoprotein antibody array and RNA-seq experiments with U87 glioblastoma cells treated with 50 mM carnosine for 24h, in order to obtain a precise and coherent picture of carnosine’s influence on signal transduction in single tumor cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110767/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434496
Series		Accession: GSE110767	ID: 200110767

675. Effect of mTORC1 and 2 inhibition on myofibroblast global gene expression 
(Submitter supplied) Background: Mechanistic target of rapamycin (mTOR) is a nodal serine/threonine protein kinase critical for the control of fundamental cellular processes. Dysregulated mTOR signalling has been shown in cancer, COPD and idiopathic pulmonary fibrosis (IPF). mTOR forms the catalytic subunit of 2 protein complexes: mTORC1 and mTORC2 which differ in upstream inputs, downstream effects and sensitivity to the allosteric inhibitor rapamycin. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 24 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102674/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA398367
Series		Accession: GSE102674	ID: 200102674

676. Identification of long noncoding RNA RP11-2B6.2 as a positive regulator of type I interferon pathway in lupus nephritis
(Submitter supplied) Methods and Materials  The high throughput RNA sequencing (RNA-seq) data from kidney biopsies of LN patients and controls was applied studied to screen for candidate lncRNAs. Quantitative real-time polymerase chain reaction(RT-qPCR) was used to detect the expression of lncRNAs and individual IFN-stimulated genes (ISGs). Western blotting and dual-luciferace luciferase reporter assay was  adopted to explore the specific function of the candidate lncRNA. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL20301 31 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98422/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA385078
Series		Accession: GSE98422	ID: 200098422

677. miR-450a acts as a tumor suppressor in ovarian cancer by readjusting energy metabolism
(Submitter supplied) Dysregulation of miRNA expression is associated with multiple diseases, including cancers where they can have oncogenic or tumor suppressive function. Here we investigated the potential tumor suppressive function of miR-450a, one of the most significantly downregulated miRNAs in ovarian cancer. RNAseq analysis revealed multipe genes involved in the epithelial-to-mesenchymal transition (EMT) were suppressed by miR-450a overexpression ovarian cancer cell line A2780. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL21290 25 Samples
FTP download: GEO (DIFF, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129076/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529911
Series		Accession: GSE129076	ID: 200129076

678. Non-coding and coding transcriptional profiles are significantly altered in pediatric Retinoblastoma tumors
(Submitter supplied) To find out the transcriptomic signature of Retinoblastoma compared to adult Retina. The methadology used was RNA sequencing using Illumina Platform.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125903/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA517916
Series		Accession: GSE125903	ID: 200125903

679. Reprogramming of Tumor-infiltrating Immune Cells in Early Stage of NSCLC
(Submitter supplied) Comparing the relative proportions of immune cells in tumor and adjacent normal tissue from NSCLC patients demonstrates the early changes of tumor immunity and provides insights to guide immunotherapy design. We mapped the immune ecosystem using computational deconvolution of bulk transcriptome data from the Cancer Genome Atlas (TCGA) and single cell RNA sequencing (scRNA-seq) data of dissociated tumors from early-stage non-small cell lung cancer (NSCLC) to investigate early immune landscape changes occurring during tumorigenesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117570/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482529
Series		Accession: GSE117570	ID: 200117570

680. Hominid-specific transposable elements and KRAB-ZFPs facilitate human embryonic genome activation and transcription in naïve hESCs
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 79 Samples
FTP download: GEO (BED, TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117395/
Series		Accession: GSE117395	ID: 200117395

681. Targeting FGFR overcomes EMT-mediated resistance in EGFR mutant non-small cell lung cancer
(Submitter supplied) Acquired drug resistance to tyrosine kinase inhibitor (TKI) targeted therapies remains a major clinical challenge. In EGFR mutant non-small cell lung cancer (NSCLC), therapeutic failure of EGFR TKIs can result from both genetic and epigenetic mechanisms of acquired drug resistance. Histologic and gene expression changes consistent with an epithelial-to-mesenchymal transition (EMT) have been associated with resistance to EGFR TKIs in both experimental models and in patients, and may coincide with genetic mechanisms of resistance such as the EGFRT790M gatekeeper mutation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114647/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472050
Series		Accession: GSE114647	ID: 200114647

682. Systematic functional characterization of BAF mutations yields novel intra-complex synthetic lethalities [RNA-Seq]
(Submitter supplied) Aberrations in genes coding for subunits of the BAF chromatin remodeling complex are highly abundant in human cancers. Currently, it is not understood how these loss-of-function mutations contribute to cancer development and how they can be targeted therapeutically. The cancer type specific occurrence patterns of certain subunit mutations suggest subunit-specific effects on BAF complex function, possibly by the formation of aberrant residual complexes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 87 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108388/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427143
Series		Accession: GSE108388	ID: 200108388

683. MYC dependent mRNA translation shapes gene expression and cell biology
(Submitter supplied) We report that MYC controls the translation of specific mRNAs in a sequence and RNA binding protein dependent manner. Specifically, using transcriptome-scale ribosome footprinting we identify 882 mRNAs whose translation depends on MYC. These mRNAs are highly significantly enriched for specific 5ÕUTR sequence motifs that bind the SRSF1/RBM42/HNRNPK complex. For example, MYC and SRFSF1/RBM42 dependent transcripts include many components of the electron transport chain and directly affect cellular respiration. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79864/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317266
Series		Accession: GSE79864	ID: 200079864

684. Wnt5a and its downstream transcription factor Stat3 are therapeutic targets for diffuse intrinsic pontine gliomas
(Submitter supplied) Understand how Wnt5a depletion affects the growth of diffuse intrinsic pontine gliomas
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130407/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA540149
Series		Accession: GSE130407	ID: 200130407

685. TNF-induced Inflammatory Genes Escape Repression in Fibroblast-like Synoviocytes: Transcriptomic and Epigenomic Analysis [RNA-seq]
(Submitter supplied) Investigated genome-wide changes in gene-expression and chromatin remodeling induced by tumour necrosis factor (TNF) in fibroblast-like synovioctyes (FLS) and macrophages to understand the contribution of FLS to the pathogenesis of rheumatoid arthritis (RA).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 5 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128638/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA528318
Series		Accession: GSE128638	ID: 200128638

686. LNK suppresses interferon signaling in melanoma
(Submitter supplied) LNK (SH2B3) is a key negative regulator of JAK-STAT signaling which has been extensively studied in malignant hematopoietic diseases. We found that LNK is significantly elevated in cutaneous melanoma; this elevation is correlated with hyperactive signaling of the RAS-RAF-MEK pathway. Elevated LNK enhances cell growth and survival in adverse conditions. Forced expression of LNK inhibits signaling by interferon-STAT1 and suppresses interferon (IFN) induced cell cycle arrest and cell apoptosis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 6 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127333/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA524699
Series		Accession: GSE127333	ID: 200127333

687. RNA seq with AML (NB4) cells upon FTO inhibition
(Submitter supplied) To determine the potential targets of FTO and identify treatment significance of FTO inhibition in AML, we conducted transcriptome wide RNA seq with NB4 cells upon DMSO and FTO inhibitors (FB23 and FB23-2) treatment.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103495/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401779
Series		Accession: GSE103495	ID: 200103495

688. RNA seq with AML cells (NB4) upon FTO knockdown
(Submitter supplied) To identify the potential targets genes of FTO in acute myeloid leukemia (AML), we peroformed RNA-seq of NB4 cells with or without FTO knockdown based on Illumina Hiseq system.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103494/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401780
Series		Accession: GSE103494	ID: 200103494

689. Neratinib, a Pan ERBB/HER Inhibitor, Restores Sensitivity of PTEN-null, BRAFV600E Melanoma to BRAF/MEK Inhibition
(Submitter supplied) The  A375, human BRAFV600E mutant melanoma, cell line (wildtype), two PTEN-null, BRAFV600E cell lines (KO5 and KO11), and PI3K overexpression cells (WT and PI3K H1047R mutant) were treated with small molecule inhibitors (dabrafenib, BRAF inhibitor; trametinib, MEK inhibitor alone and in combination for 0, 1 and 7 days
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 30 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130396/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA539979
Series		Accession: GSE130396	ID: 200130396

690. Transcriptional changes in the breast cancer cell line MCF7 rendered resistant to the cationic drug siramesine
(Submitter supplied) Repurpusing cationic amphiphilic drugs (CADs) may be enhance the effect of chemotherapy in cancer treatment. In order to understand the molecular mechanism, we created cell lines resistant to the CAD siramesine by growing them for 6 months in increasing concentrations of siramesine. Parental and resistant cell lines were subjected to RNAseq and revealed diffentially expressed genes in ca+ and cAMP signalling pathways.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 5 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130363/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA539897
Series		Accession: GSE130363	ID: 200130363

691. WaGa single cell RNA sequencing
(Submitter supplied) The Merkel cell carcinoma cell line (MCC) WaGa was sequenced using the 10x Genomics 3' Chromium v2.0 platform in order to analyse transcriptional heterogeneity on a single cell level
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 1 Sample
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130346/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA535920
Series		Accession: GSE130346	ID: 200130346

692. Atypical function of a centrosomal module in WNT signalling drives contextual cancer cell motility
(Submitter supplied) Centrosomes control cell motility, polarity and migration that are thought to be mediated by their microtubule-organizing capacity. In this study we demonstrate that WNT signalling drives a distinct form of non-directional cell motility that requires a key centrosome module, but not microtubules or centrosomes.  Upon exosome mobilization of Planar Cell Polarity proteins, we show that DVL2 orchestrates recruitment of a CEP192-PLK4/AURKB complex to the cell cortex where PLK4/AURKB act redundantly to drive protrusive activity and cell motility. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 120 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129871/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA534108
Series		Accession: GSE129871	ID: 200129871

693. m7G methylation by METTL1 regulates let-7 microRNAs [m7G-RIP-Seq KD A549]
(Submitter supplied) Methylation of N7-methylguanosine (m7G) is found at mRNA caps and at defined internal positions within abundant tRNAs and rRNAs. However, its detection within low abundance mRNAs and microRNAs (miRNAs) has been hampered by lack of sensitive detection strategies. Here, we adapt a chemical reactivity assay to detect internal m7G in RNA from eukaryotic cells. Using this approach, alongside a confirmational RNA immunoprecipitation assay, we identify m7G within miRNAs inhibiting cell migration, and show that METTL1 mediates this m7G methylation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120455/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA493090
Series		Accession: GSE120455	ID: 200120455

694. In vivo generation of post-infarct human cardiac muscle by laminin-promoted cardiovascular progenitors [H1 differentiation protocol]
(Submitter supplied) Regeneration of injured human heart muscle is limited and an unmet clinical need. There are no methods for the reproducible generation of clinical quality stem-cell-derived cardiovascular progenitors (CVPs). We identified laminin-221 (LN-221) as the most likely expressed cardiac laminin. We produced it as human recombinant protein, and showed that LN-221 promotes differentiation of pluripotent hESCs towards cardiomyocyte lineage and downregulates pluripotency and teratoma associated genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 44 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101132/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393784
Series		Accession: GSE101132	ID: 200101132

695. In vivo generation of post-infarct human cardiac muscle by laminin-promoted cardiovascular progenitors [LN-521 or LN-521+LN-221]
(Submitter supplied) Regeneration of injured human heart muscle is limited and an unmet clinical need. There are no methods for the reproducible generation of clinical quality stem-cell-derived cardiovascular progenitors (CVPs). We identified laminin-221 (LN-221) as the most likely expressed cardiac laminin. We produced it as human recombinant protein, and showed that LN-221 promotes differentiation of pluripotent hESCs towards cardiomyocyte lineage and downregulates pluripotency and teratoma associated genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101076/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393685
Series		Accession: GSE101076	ID: 200101076

696. In vivo generation of post-infarct human cardiac muscle by laminin-promoted cardiovascular progenitors [HS1001 differentiation protocol]
(Submitter supplied) Regeneration of injured human heart muscle is limited and an unmet clinical need. There are no methods for the reproducible generation of clinical quality stem-cell-derived cardiovascular progenitors (CVPs). We identified laminin-221 (LN-221) as the most likely expressed cardiac laminin. We produced it as human recombinant protein, and showed that LN-221 promotes differentiation of pluripotent hESCs towards cardiomyocyte lineage and downregulates pluripotency and teratoma associated genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 34 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100722/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA392969
Series		Accession: GSE100722	ID: 200100722

697. BET protein proteolysis targeting chimera (PROTAC) exerts potent lethal activity against Mantle Cell Lymphoma cells
(Submitter supplied) Bromodomain extraterminal protein (BETP) inhibitors transcriptionally repress oncoproteins and NFkB target genes, which undermines the growth and survival of MCL cells. However, BETi treatment causes accumulation of BETPs, associated with reversible binding and incomplete inhibition of BRD4, which potentially compromises the activity of BETi in MCL cells. Unlike BETi, BET-PROTACs (proteolysis-targeting chimera) ARV-825 and ARV-771 (Arvinas, Inc.) recruit and utilize an E3-ubiquitin ligase to effectively degrade BETPs in MCL cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 12 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98268/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384509
Series		Accession: GSE98268	ID: 200098268

698. Next Generation Sequencing Quantitative Analysis of HepG2, hyper-glycolytic model cell, oxamate treated cells
(Submitter supplied) To determine the genes potentially responsible for the lactate-mediated gene expression regulation in hepatocellular carcinoma, we performed RNA-seq analyses on parental HepG2, HepG2/metR and oxamate-treated HepG2/metR cells. To gain mechanistic insights into the lactate-induced pro-migratory phenotypes, we established a cell model that acquired a resistance to metformin while producing lactate at a high level by selecting HepG2 cells that survived a chronic exposure to metformin for more than 5 months (HepG2/metR). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125525/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516665
Series		Accession: GSE125525	ID: 200125525

699. Synergy between variant PRC1 complexes defines Polycomb-mediated gene repression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus; Drosophila melanogaster
Type:		Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL19415 GPL25537 380 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119620/
Series		Accession: GSE119620	ID: 200119620

700. Generation, transcriptome profiling, and functional validation of single cells from cone-enriched human retinal organoids
(Submitter supplied) The macula of the retina has a high ratio of cones to rods and is critical for central vision and visual acuity. Here we report the generation, transcriptome profiling, and functional validation of single cells from cone-enriched human retinal organoids differentiated from hESCs.  Single-cell RNA-seq of 8-month retinal organoids identified clusters of cone and rod photoreceptors and confirmed the cone enrichment initially revealed by immunostaining. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 1346 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119343/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488818
Series		Accession: GSE119343	ID: 200119343

701. Generation, transcriptome profiling, and functional validation of cone-enriched human retinal organoids
(Submitter supplied) The macula of the retina has a high ratio of cones to rods and is critical for central vision and visual acuity. Macula degenerations affect vision the most and are incurable. Here we report the generation, transcriptome profiling, and functional validation of cone-enriched human retinal organoids differentiated from hESCs. Transcriptome profiling using bulk RNA-seq demonstrated that retinal differentiation in vitro recapitulated retinogenesis in vivo in the temporal expression of cell differentiation markers and retinal disease genes, as well as in mRNA alternative splicing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119274/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488663
Series		Accession: GSE119274	ID: 200119274

702. Genome-wide profiling of cervical RNA-binding proteins identified HPV regulation of RNASEH2A expression by viral E7 and E2F1
(Submitter supplied) RNA-binding proteins (RBPs) have been shown to control mRNA processing, stability, transport, editing and translation. Application of large-scale quantitative technologies has facilitated genome-wide identification of RBPs and linked their defects to human diseases and carcinogenesis. We have recently conducted transcriptome analysis comparing normal cervical tissues with HPV-positive cervical cancer tissues by using two different RNA-seq platforms. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113942/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454568
Series		Accession: GSE113942	ID: 200113942

703. Selective Inhibition of the Second Bromodomain of BET Family Maintains Anti-Tumor Efficacy and Improves Tolerability
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 10 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130269/
Series		Accession: GSE130269	ID: 200130269

704. Stromal Fibroblasts Drive Single Cell Heterogeneity in Pancreatic Cancer
(Submitter supplied) To understand the interplay between cancer and stroma, we performed single cell RNA-sequencing of PDAC cells admixed with stromal fibroblasts and defined different single cell populations with varying levels of proliferative and metastatic transcriptional states. PDAC cell behavior in vitro and in vivo on these phenotypic axes could be tuned with the proportion of stromal fibroblasts. These cell types were identified in human pancreatic tumors, and specific subpopulations were associated with worsened outcomes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 189 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113616/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA464359
Series		Accession: GSE113616	ID: 200113616

705. Mapping the chemotherapy-induced RNA interactome in Glioblastoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL16791 48 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98128/
Series		Accession: GSE98128	ID: 200098128

706. Mapping the chemotherapy-induced RNA interactome in Glioblastoma [RNA-Seq]
(Submitter supplied) Long non-coding RNAs (lncRNAs) are increasingly recognized as important players in transcription and epigenetic-driven cell diversification. So far, lncRNA function in more dynamic transcriptional reprogramming, i.e drug response, has been largely unexplored. Here, we investigated the regulatory circuits induced by chemotherapy in glioblastoma, the most aggressive and clinically refractory brain cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98126/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384285
Series		Accession: GSE98126	ID: 200098126

707. Single cell RNA sequencing analysis of fresh resected human lung tissue
(Submitter supplied) Fresh resected human lung tissue (parenchymal lung and distal airway specimens) was obtained via the CPC BioArchive at the Comprehensive Pneumology Center Munich (CPC-M, Munich, Germany) and profiled using single cell RNA sequencing technology (Drop-seq). In total, we analysed parenchymal tissue of uninvolved areas of tumour resection material from four patients.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (CSV, RDATA, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130148/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA534093
Series		Accession: GSE130148	ID: 200130148

708. ETV4 is necessary for estrogen signaling and growth in endometrial cancer cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 25 Samples
FTP download: GEO (BEDGRAPH, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129805/
Series		Accession: GSE129805	ID: 200129805

709. ETV4 is necessary for estrogen signaling and growth in endometrial cancer cells [RNA-seq]
(Submitter supplied) Estrogen signaling through estrogen receptor alpha (ER) plays a major role in endometrial cancer risk and progression; however, the molecular mechanisms underlying ER’s regulatory role in endometrial cancer are poorly understood. In breast cancer cells, ER genomic binding is enabled by FOXA1 and GATA3, but the transcription factors that control ER genomic binding in endometrial cancer cells remain unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129804/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA532874
Series		Accession: GSE129804	ID: 200129804

710. Single-cell RNA sequencing on breast cancer cells enriched for cancer stem cell properties using functional assays
(Submitter supplied) We used mammosphere formation assay and label-retention assay as functional cellular approaches to enrich for cells with different degree of cancer stem cell properties in the breast cancer cell line MDA-MB-231 and performed single-cell RNA sequencing
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 121 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124989/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA514740
Series		Accession: GSE124989	ID: 200124989

711. Targeting the perivascular niche sensitizes disseminated tumour cells to chemotherapy
(Submitter supplied) The presence of disseminated tumour cells (DTCs) in bone marrow predicts poorer metastasis-free survival of breast cancer patients with localized disease, and their eradication improves long-term prognosis. DTCs persist in distant tissues despite administration of adjuvant chemotherapy, ostensibly because the majority of DTCs are quiescent. Here, we provide evidence that the microenvironment of DTCs protects them from chemotherapy independent of cell cycle status. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119153/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488272
Series		Accession: GSE119153	ID: 200119153

712. Notch signalling mediates secondary senescence
(Submitter supplied) Oncogene induced senescence (OIS) is a tumour suppressive response to oncogene activation that can be transmitted to neighbouring cells through secreted factors of the senescence associated secretory phenotype (SASP). Using single-cell transcriptomics we observed two distinct endpoints, a primary marked by Ras and a secondary by Notch. We find that secondary senescence in vitro and in vivo requires Notch, rather than SASP alone as previously thought. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
4 related Platforms 1163 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115301/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474503
Series		Accession: GSE115301	ID: 200115301

713. An siRNA screen identifies CHD4 as a target for epigenetic therapy
(Submitter supplied) AIM: We performed RNA-sequencing experiments seeking genes whose expression changed after siCHD4 treatment. METHOD: We generated cDNA libraries from RNA purified from SW48 treated by siNegative control, siCHD4, siNegative control plus siDNMT1, siCHD4 plus siDNMT1, siCHD4 plus Decitabine and siNegative control plus Decitabine. We sequenced the cDNA libraries generating single end 50 bp reads on the illumina HiSeq 2500 platform. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62804/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA265187
Series		Accession: GSE62804	ID: 200062804

714. Diverse Compounds from Pleuromutilin Lead to a Thioredoxin Inhibitor and Inducer of Ferroptosis
(Submitter supplied) The chemical diversification of natural products provides a robust and general method for creation of stereochemically rich and structurally diverse small molecules. The resulting compounds have physicochemical traits different from those in most screening collections, and as such are an excellent source for biological discovery. Herein, we subject the diterpene natural product pleuromutilin to reaction sequences focused on creating ring system diversity in few synthetic steps. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 8 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126868/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA523577
Series		Accession: GSE126868	ID: 200126868

715. Combined MEKi (GDC-0973) and WNT (G007-LK) treatment in APC and KRAS mutant HCT-15 cell line
(Submitter supplied) We report RNAseq data from HCT-15 cells were treated wih control(DMSO), GDC-0973, G007-LK and combined GDC-0973 and G007-LK treatmetn for 24 hours.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123807/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509901
Series		Accession: GSE123807	ID: 200123807

716. Quiescent glioblastoma cells shift to an epithelial-mesenchymal transition-like gene program
(Submitter supplied) Quiescent stem cells of glioblastoma (GBM), a malignant primary brain tumor, are potential sources for recurrence after therapy. However, the gene expression program underlying the physiology of GBM stem cells remains unclear. We have isolated quiescent GBM cells by engineering them with a knock-in H2B-GFP proliferation reporter and expanding them in a 3D tumor organoid model that mimics tumor heterogeneity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114574/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471821
Series		Accession: GSE114574	ID: 200114574

717. Intracerebral Hemorrhage Induces Inflammatory Gene Expression in Peripheral Blood: Global Transcriptional Profiling in ICH Patients
(Submitter supplied) Intracerebral hemorrhage (ICH) is a severe neurological disorder with no proven treatment. While there is substantial interest in post-ICH neuroinflammation and associated pathophysiological mechanisms, these processes remain poorly understood. To further advance our understanding, we performed RNA-seq in the peripheral blood of ICH patients to test the hypothesis that ICH would induce inflammatory biological pathways. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 22 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125512/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516650
Series		Accession: GSE125512	ID: 200125512

718. PD-1/PD-L1 immune checkpoint and p53 loss facilitate tumor progression in activated B cell diffuse large B-cell lymphomas
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Expression profiling by array; Other
Platforms: GPL15088 GPL16417 GPL21103 33 Samples
FTP download: GEO (FASTA, PAIR, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116290/
Series		Accession: GSE116290	ID: 200116290

719. Targetable genetic alterations of TCF4 (E2-2) drive immunoglobulin expression in the activated B-cell subtype of diffuse large B-cell lymphoma.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119477/
Series		Accession: GSE119477	ID: 200119477

720. Differential gene expression analysis in BRD4-PROTAC treated diffuse large B-cell lymphoma cell lines
(Submitter supplied) We identified differential gene expression after treatment with BRD4-PROTAC ARV771 in two ABC-like diffuse large B-cella lymphoma cell lines. We have identified cluster of gene expression regulated after BRD4 inhibition which are criticaly important for DLBCL malignancy.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119241/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488595
Series		Accession: GSE119241	ID: 200119241

721. A temporal proteogenomic atlas of HCV-host interactions unravels cell circuits driving viral and metabolic liver disease.
(Submitter supplied) Background and aims: Hepatitis C virus (HCV) infection is a major cause of liver disease including steatosis, fibrosis and liver cancer. Viral cure cannot fully eliminate the risk of disease progression and hepatocellular carcinoma (HCC) in advanced liver disease. The mechanisms for establishment of infection, liver disease progression and hepatocarcinogenesis are only partially understood. To address these questions, we probed the functional proteogenomic architecture of HCV infection within a hepatocyte-model. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 63 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126831/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA523419
Series		Accession: GSE126831	ID: 200126831

722. Next generation sequencing analysis of mRNA profile in cisplatin-resistant gastric cancer cell line SGC7901
(Submitter supplied) Cisplatin-resistant gastric cancer (GC) occurs in patients with GC treated with cisplatin-based chemotherapy, which results in disease progression and early recurrence during the treatment. To understand the initiation and developmental mechanism underlying cisplatin-resistant GC, we developed cisplatin resistant SGC7901 cells (SGC7901/DDP) from the parental cells (SGC7901/S) by continuous exposure to increasing concentrations of cisplatin and subjected these two cell lines to RNA sequencing analysis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122130/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA503804
Series		Accession: GSE122130	ID: 200122130

723. Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [RNA-seq]
(Submitter supplied) Transcriptomic profiling of human breast tumors using RNA sequencing
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 23 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100799/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393113
Series		Accession: GSE100799	ID: 200100799

724. Integrated high-throughput screen to identify novel treatment leads for pediatric acute myeloid leukemia (AML)
(Submitter supplied) AML cell lines that underwent high throughput drug screening had baseline RNA sequencing done for the purpose of gene expression studies
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126489/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA522070
Series		Accession: GSE126489	ID: 200126489

725. Transcriptomic analysis of the role of the integrin a6b4 in detached cells
(Submitter supplied) Analysis of gene expression profiles of matrix-detached cells with and without expression of ITGB4, in clustering and non-clustering conditions. The experiment tested the hypothesis that the integrin beta 4 (ITGB4) mediates a significant amount of pro-survival signaling in matrix-detached conditions. Expression of ITGB4 in cancer is correlated with poor patient survival and is impliated in increased metastatic spread. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115059/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA473581
Series		Accession: GSE115059	ID: 200115059

726. Characterisation of the myeloid differentiation process of human hematopoietic stem cells
(Submitter supplied) Hematopoietic stem cells (HSCs) can self-renew and/or differentiate into various functionally divergent progenitor cell types, such as common myeloid progenitors (CMPs), megakaryocyte-erythrocyte progenitors (MEPs) or granulocyte-macrophage progenitors (GMPs). When the process of self-renewal and differentiation is altered, e.g. upon genetic or epigenetic changes in HSCs, abnormal (pre)leukemic stem cell subpopulations may form, eventually resulting in the onset of hematological malignancies. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113182/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450387
Series		Accession: GSE113182	ID: 200113182

727. An RNA-centric dissection of host complexes controlling flavivirus infection
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL18573 26 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109194/
Series		Accession: GSE109194	ID: 200109194

728. An RNA-centric dissection of host complexes controlling flavivirus infection [irCLIP]
(Submitter supplied) Flaviviruses including dengue virus (DENV) and Zika virus (ZIKV) cause significant human disease. Co-opting cellular factors for viral protein translation and viral genome replication at the endoplasmic reticulum (ER) is a shared replication strategy, despite different clinical outcomes. While the protein products of these viruses have been studied in depth, how the RNA genomes operate inside human cells is poorly understood. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109191/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA430089
Series		Accession: GSE109191	ID: 200109191

729. An RNA-centric dissection of host complexes controlling flavivirus infection [RNA-Seq]
(Submitter supplied) Flaviviruses including dengue virus (DENV) and Zika virus (ZIKV) cause significant human disease. Co-opting cellular factors for viral protein translation and viral genome replication at the endoplasmic reticulum (ER) is a shared replication strategy, despite different clinical outcomes. While the protein products of these viruses have been studied in depth, how the RNA genomes operate inside human cells is poorly understood. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109190/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA430086
Series		Accession: GSE109190	ID: 200109190

730. Overexpression of HDAC8 establishes a unique gene signature in BRAF-mutant melanoma cells
(Submitter supplied) Systems level analyses using mass spectrometry-based phosphoproteomics and RNA-Seq implicated HDAC8 in the regulation of MAPK and AP-1 signaling pathways. Introduction of HDAC8 into drug-naïve melanoma cells conveyed resistance both in vitro and in in vivo xenograft models. HDAC8-mediated BRAF inhibitor resistance was mediated via receptor tyrosine kinase (RTK) activation leading to Ras/CRAF/MEK/ERK signaling. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127564/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA524923
Series		Accession: GSE127564	ID: 200127564

731. Antisense lncRNA transcription mediates DNA demethylation to drive stochastic Protocadherin α promoter choice
(Submitter supplied) Stochastic activation of clustered Protocadherin (Pcdh) α, β, and γ genes generates a cell-surface identity code in individual neurons that functions in neural circuit assembly. Here, we show that Pcdhα gene choice involves the activation of an antisense promoter located in the first exon of each Pcdhα alternate gene. Transcription of an antisense long noncoding RNA (lncRNA) from this antisense promoter extends through the sense promoter, leading to DNA demethylation of the CTCF binding sites proximal to each promoter. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL21697 GPL21626 72 Samples
FTP download: GEO (BW, HIC) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115862/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476330
Series		Accession: GSE115862	ID: 200115862

732. Global donor and acceptor splicing site kinetics in human cells
(Submitter supplied) Transient transcriptome sequencing and kinetic modeling suggest how the kinetics and yield of RNA splicing are encoded in the human genome.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 28 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129635/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481857
Series		Accession: GSE129635	ID: 200129635

733. High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer
(Submitter supplied) The dynamic nature of chromatin and transcription plays a critical role in normal differentiation and is expected to contribute to tumor evolution. Studying chromatin heterogeneity with single-cell resolution is mandatory to understand the role of epigenetic plasticity in cancer. Here, we describe a droplet microfluidics system that enables the profiling of chromatin marks of individual cells with an average coverage of up to 10,000 loci per cell. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL22245 GPL19415 GPL18573 10 Samples
FTP download: GEO (FASTA, TAR, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117309/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481734
Series		Accession: GSE117309	ID: 200117309

734. Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models
(Submitter supplied) We report the expression profiles of 21 T- and NK-cell lymphomas to provide a platform for further investigation of targetable vulnerabilities in diseases represented by these cell lines
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 21 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114085/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472977
Series		Accession: GSE114085	ID: 200114085

735. Inhibition of MYC by the SMARCB1 tumor suppressor
(Submitter supplied) We report that the protein encoded by the SMARCB1 gene, SNF5, is capable of inhibiting MYC binding in vitro and in a malignant rhabdoid tumor (MRT) cell line. By comparing the effects of reintroduction of SNF5 with genetic inhibition of MYC (OMOMYC) on multiple aspects of chromatin remodeling and transcription in MRT cells, we show that regulation of MYC binding by SNF5 is not connected to the role of SNF5 in chromatin remodeling, but instead is responsible for controlling RNA polymerase pause release during transcription. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 30 Samples
FTP download: GEO (NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109310/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA430400
Series		Accession: GSE109310	ID: 200109310

736. MULTI-seq: Universal sample multiplexing for single-cell RNA sequencing using lipid-tagged indices
(Submitter supplied) We report the development of MULTI-seq: a scRNA-seq and snRNA-seq sample multiplexing approach using lipid- or cholesterol-modified oligonucleotides. We demonstrate MULTI-seq utility in the following scRNA-seq and snRNA-seq contexts: (1) Live HEKs and HMECs with and without stimulation with TGF-β, (2) Purified nuclei from HEKs, MEFs, and Jurkats stimulated for 0-24 hrs with ionomycin and PMA, (3) 96 unique HMEC cultures (with one technical replicate), and (4) human metastases and mouse immune cells isolated from cryopreserved primary tissue samples dissected from a patient-derived xenograft mouse model of triple-negative breast cancer at progressive stages of metastasis to the lung.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
4 related Platforms 24 Samples
FTP download: GEO (MTX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129578/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA531855
Series		Accession: GSE129578	ID: 200129578

737. Transcriptomically-guided mesendoderm induction of human pluripotent stem cells using a systematically defined culture scheme
(Submitter supplied) Human pluripotent stem cells (hPSCs) are an essential cell source in tissue engineering, studies of development, and disease modeling.  Efficient and broadly amenable protocols for rapid lineage induction of hPSCs are of great interest in the stem cell biology field.  We describe a simple yet robust method for differentiation of hPSCs into mesendoderm in defined conditions utilizing single-cell seeding and BMP4 and Activin A (BA) treatment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 35 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129570/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA531831
Series		Accession: GSE129570	ID: 200129570

738. Comprehensive gene expression analysis of TNF-alpha-stimulated human umbilical vein endothelial cells (HUVECs)
(Submitter supplied) Lysine 9 di-methylation and lysine 27 tri-methylation of histone H3 (H3K9me2 and H3K27me3) are mostly linked to gene repression. However, functions of repressive histone methylation dynamics during inflammatory responses remain poorly understood. Here, we show that lysine demethylase 7A (KDM7A) and 6A (UTX) are rapidly transported to nuclear factor kappa-B (NF-κB) related elements in human endothelial cells in response to tumor necrosis factor (TNF)-α. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 29 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121958/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA501792
Series		Accession: GSE121958	ID: 200121958

739. Impact of a pre-operative exercise intervention on breast cancer proliferation and gene expression
(Submitter supplied) RNAseq analysis of primary breast cancer samples
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 64 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129508/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA531611
Series		Accession: GSE129508	ID: 200129508

740. Regulation of hypoxia-inducible factor activity by ZMYND8
(Submitter supplied) ZMYND8 coactivates the global HIF target genes in breast cancer MDA-MB-231 cells.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18573 20 Samples
FTP download: GEO (BED, BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108833/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA428761
Series		Accession: GSE108833	ID: 200108833

741. Transcriptome-wide binding profile of RNA-binding protein HuR and its inhibitor in MDA-MB-231 cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 8 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129530/
Series		Accession: GSE129530	ID: 200129530

742. Single cell transcriptomics of human and mouse lung cancers reveals conserved myeloid populations across individuals and species
(Submitter supplied) Tumor-infiltrating myeloid cells (TIMs) comprise monocytes, macrophages, dendritic cells and neutrophils, and have emerged as key regulators of cancer growth. These cells can diversify into a spectrum of states, which may promote or limit tumor outgrowth, but remain poorly understood. Here, we used single-cell RNA sequencing to map TIMs in non-small cell lung cancer patients. We uncovered 25 TIM states, most of which were reproducibly found across patients. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 40 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127465/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA524857
Series		Accession: GSE127465	ID: 200127465

743. Chromatin remodeling mediated by ARID1A is indispensable for normal hematopoiesis in mice (human RNA-Seq)
(Submitter supplied) ARID1A is a component of the mammalian SWI/SNF complex involved in chromatin remodeling. A functional SWI/SNF complex is required for diverse physiological processes including hematopoiesis, however, the precise role played by ARID1A in hematopoietic development is unclear. Here we utilize hematopoietic cell-specific deletion of Arid1a in mice to uncover its role during adult hematopoiesis. We demonstrate that ARID1A is essential for maintaining the frequency and function of hematopoietic stem cells and its loss impaired the differentiation of both myeloid and lymphoid lineages. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125848/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA517704
Series		Accession: GSE125848	ID: 200125848

744. Temporal dynamic reorganization of 3D chromatin in hormone-induced breast cancer and endocrine resistance
(Submitter supplied) To establish a data-driven learning model of the temporal dynamics and 3D chromatin reorganization, we conducted tethered chromatin conformation (TCC) sequencing to examine 3D structure dynamics in estradiol (E2)-induced breast cancer MCF7 cells and Tamoxifen resistant breast cancer MCF7 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 60 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108787/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA428600
Series		Accession: GSE108787	ID: 200108787

745. Transcriptomic hallmarks of tumor plasticity and stromal interactions in brain metastasis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL22245 GPL16791 48 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115702/
Series		Accession: GSE115702	ID: 200115702

746. Transcriptomic hallmarks of tumor plasticity and stromal interactions in brain metastasis [MultiDisease]
(Submitter supplied) We report that well-defined xenograft models of leading sources of CNS metastasis (melanoma, breast cancer, lung cancer) undergo specific transcriptomic alterations upon entering the brain microenvironment. This dataset can be utilized to explore the mechanisms of tumor cell plasticity as well as the co-adaptation of the brain microenvironment to metastatic disease.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL22245 GPL17021 22 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115701/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475788
Series		Accession: GSE115701	ID: 200115701

747. Transcriptomic hallmarks of tumor plasticity and stromal interactions in brain metastasis [BrainMet_SQ_2D]
(Submitter supplied) We find that malignant LUAD tumor cells grown in the brain microenvironment display significantly altered transcriptomic profiles when compared to tumor cells grown in monolayer or subcutaneously. Additionally, we characterize the reciprocal neuroinflammatory response of the surrounding brain stroma to metastatic LUAD. This dataset can be utilized to explore the mechanisms of LUAD cell plasticity as well as the co-adaptation of the brain microenvironment to metastatic disease.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL22245 21 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115700/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475787
Series		Accession: GSE115700	ID: 200115700

748. Transcriptomic hallmarks of tumor plasticity and stromal interactions in brain metastasis [BrainMet_Othotopic]
(Submitter supplied) We find that malignant LUAD tumor cells grown in the brain microenvironment display significantly altered transcriptomic profiles when compared to tumor cells grown in monolayer or subcutaneously. Additionally, we characterize the reciprocal neuroinflammatory response of the surrounding brain stroma to metastatic LUAD. This dataset can be utilized to explore the mechanisms of LUAD cell plasticity as well as the co-adaptation of the brain microenvironment to metastatic disease.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platform: GPL22245 5 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115699/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475786
Series		Accession: GSE115699	ID: 200115699

749. Transcriptional and chromatin profiles of duodenum epithelium upon HNF4 loss in mice by RNA-seq and ChIP-seq
(Submitter supplied) We find that HNF4G is an intestine-particular HNF4 paralog, and works redundantly with HNF4A for driving intestinal differentiation by controlling chromatin accessibility and regulating thousands of transcripts particular to differentiated cells. Without HNF4s, cells fail to achieve a differentiated state. A positive feedback loop between HNF4 transcriptional regulation and BMP/SMAD signaling stabilizes differentiation, and the two inputs cooperatively activate differentiation gene expression.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms 33 Samples
FTP download: GEO (BED, BW, DIFF, H5) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112946/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA449547
Series		Accession: GSE112946	ID: 200112946

750. Genome-wide analysis of PDAC Pa03c cells upon lipoprotein depletion
(Submitter supplied) To assay differently expressed genes in PDAC cells Pa03c cultured in regular 10% FBS medium or lipoprotein depleted 10% LPDS medium
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10904 2 Samples
FTP download: GEO (IDAT, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129432/
Series		Accession: GSE129432	ID: 200129432

751. Transcriptome sequencing analysis of BRAF-mutant melanoma metastases.
(Submitter supplied) Melanoma patients carry a high risk of developing brain metastases, and improvements in survival are still measured in weeks or months. Durable disease control within the brain is impeded by poor drug penetration across the blood-brain barrier, as well as intrinsic and acquired drug resistance. In this study, we used high-throughput pharmacogenomic profiling to identify potentially repurposable compounds against BRAF-mutant melanoma brain metastases. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100066/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA390619
Series		Accession: GSE100066	ID: 200100066

752. Transcriptome-wide effect profile of HuR inhibitor KH-3
(Submitter supplied) The purpose of this study is to generate mRNA effect profle of KH-3, an inhibitor of RNA-binding protein HuR, in human breast cancer cell line MDA-MB-231 cells by RNA sequencing. Total RNA from cells treated with DMSO or KH-3 was collected for library prepareation and deep sequencing, in duplicate, using Illumina Hiseq 2500 system.  About 30 million sequence reads per sample were mapped against the transcript databases annotated in GENCODE v24 using STAR default parameters. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129362/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA531021
Series		Accession: GSE129362	ID: 200129362

753. Differential lncRNA expression upon hypoxia affects splicing efficiency
(Submitter supplied) RNA sequencing was performed to identify long non-coding RNAs that are dysregulated upon hypoxia in breast cancer. Subsequently, the effect on splicing effiency (intron retention, exon skipping …) was investigated from RNA sequencing analysis upon knockdown of the candidate lncRNA and upon hypoxia.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129344/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA530983
Series		Accession: GSE129344	ID: 200129344

754. Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression
(Submitter supplied) Background: Global DNA methylation alterations are hallmarks of cancer. The tumor-suppressive TET enzymes, which are involved in DNA demethylation, are decreased in prostate cancer (PCa); in particular, TET2 is specifically targeted by androgen-dependent mechanisms of repression in PCa and may play a central role in carcinogenesis. Thus, identification of key genes targeted by TET2 dysregulation may provide further insight into cancer biology. more...
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128399/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA527318
Series		Accession: GSE128399	ID: 200128399

755. FLT3-N676K drives acute myeloid leukemia in a xenograft model of KMT2A-MLLT3 leukemogenesis
(Submitter supplied) Activating signaling mutations are common in acute leukemia with KMT2A (previously MLL) rearrangements. Herein, we show that co-expression of FLT3-N676K and KMT2A-MLLT3 in human CD34+ cord blood cells primarily cause acute myeloid leukemia (AML) and rarely acute lymphoblastic leukemia (ALL) in immunodeficient mice. By contrast, expression of KMT2A-MLLT3 alone cause ALL, double-positive leukemia (DPL, expressing both CD33 and CD19), or bilineal leukemia (BLL, comprised of distinct myeloid and lymphoid leukemia cells), and rarely AML. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 31 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127492/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA524875
Series		Accession: GSE127492	ID: 200127492

756. Mutated H3 Histones Drive Human Pre-Leukemic Hematopoietic Stem Cell Expansion And Promote Leukemic Aggressiveness
(Submitter supplied) Leukemogenesis is a stepwise progression from mutated, pre-neoplastic hematopoietic stem cells (HSCs) to full-blown leukemia. Our ability to prevent or treat de novo and secondary acute myeloid leukemia (AML) is limited by our incomplete understanding of the epigenetic disruption that is central to this process, including improper histone methylation. We performed a comprehensive analysis of 16 histone H3 genes in 434 primary acute myeloid leukemia (AML) samples and identified mutations in adult and pediatric cases (1.6%), with a higher incidence in secondary AML (s-AML) (9%). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL20301 38 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122273/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA504437
Series		Accession: GSE122273	ID: 200122273

757. Studying the selectivity of a targeted small molecule degrading a hypoxia-associated non-coding RNA
(Submitter supplied) Small molecule targeted recruitment of nucleases to RNA is a powerful method to affect RNA biology.  Inforna, a sequence-based design approach to target RNA, enables the design of small molecules that bind and cleave RNA in a selective and substoichiometric manner.  Herein, we investigate the ability of RNA targeted degradation to improve the selectivity of small molecules targeting RNA.  The microRNA-210 hairpin precursor (pre-miR-210) is overexpressed in hypoxic cancers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129307/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA530777
Series		Accession: GSE129307	ID: 200129307

758. Illumina sequencing analysis of LINC00998 knockdown and control in Huh7 cell line
(Submitter supplied) shRNA knockdown against LINC00998 in Huh7 cells followed by RNA-seq. LINC00998 is also known as SMIM30 or ENSG00000214194.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129277/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA530711
Series		Accession: GSE129277	ID: 200129277

759. RNA-SEQ Quantitative Analysis of WT and Mpl-del-overexpressing AMKL cell Transcriptomes
(Submitter supplied) In the previous studies, we reported that Mpl alternative splicing form Mpl-del overexpressed in acute megakaryoblasttic leukemia (AMKL) patients and mediated thrombopoietin signaling to promote AMKL cells malignant proliferation and chemotherapy resisitance. To investigate the detailed mechanism of Mpl-del mediated AMKL cells proliferation and survival, the AMKL cell Dami stably expressing GFP or Mpl-del-GFP were established by transduction with GFP or Mpl-del-GFP lentiviruses and treated with 20ng/ml TPO for RNA-SEQ analysis to examine the expression of proliferation and survival-related genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127762/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA525352
Series		Accession: GSE127762	ID: 200127762

760. Unleashing Type-2 Dendritic Cells
(Submitter supplied) Singe-cell transcriptomic profiling of myeloid cells from mouse and human tumor-draining lymph nodes
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL21103 GPL26102 3 Samples
FTP download: GEO (MTX, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125680/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA517156
Series		Accession: GSE125680	ID: 200125680

761. MTHFD1 links folate metabolism to BRD4-mediated transcriptional regulation
(Submitter supplied) The histone acetyl-reader BRD4 is an important regulator of chromatin structure and transcription, yet factors modulating its activity have remained elusive. Here we describe two complementary screens for functional regulators and physical interactors of BRD4, which converge on the folate pathway enzyme MTHFD1. We show that a fraction of MTHFD1 resides in the nucleus, where it is recruited to distinct genomic loci by direct interaction with BRD4. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL21290 128 Samples
FTP download: GEO (BIGWIG, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE105nnn/GSE105786/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA415413
Series		Accession: GSE105786	ID: 200105786

762. Transcriptome wide identification of retained introns upon depletion of the splicing factors WBP11 or SNW1
(Submitter supplied) We identified introns that are dependent on WBP11 or SNW1 for efficient splicing. WBP11 and SNW1 were depleted by RNAi and compared to a mock transfected population of cells. WBP11 was also depleted by auxin and compared to an untreated population of cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129231/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA530564
Series		Accession: GSE129231	ID: 200129231

763. H2A.Z overexpression suppresses senescence and chemosensitivity in pancreatic ductal adenocarcinoma
(Submitter supplied) Pancreatic ductal adenocarcinoma is one of the most intractable and devastating of all malignant tumors. Epigenetic modifications involving both DNA methylation and histone modification have a relationship between tumor initiation and progression. However, the contribution of histone variants in the PDAC is unknown. Here, we demonstrated that the histone variant H2A.Z is highly expressed in PDAC cell lines and PDAC patients and its overexpression correlated with poor prognosis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129182/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA530404
Series		Accession: GSE129182	ID: 200129182

764. Identification of m6dA in genomic DNA and transcriptional patterns in human genomes by DIP-Seq and RNAseq
(Submitter supplied) We identify m6dA in human genomic DNA by DNA immunoprecipitation and subsequent Hi-Throughput Illumina sequencing (DIP-Seq). We use a dA6m specific antibody for DNA pulldown, and input as control. In addition, we performed RNA High Throughput Illumina Sequencing on biologically matched samples. This data supplements our analysis of already published data.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL20301 9 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123065/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA507429
Series		Accession: GSE123065	ID: 200123065

765. PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL6246 GPL18573 GPL19057 32 Samples
FTP download: GEO (BW, CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120478/
Series		Accession: GSE120478	ID: 200120478

766. PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription.[RNA-seq and ChIP-seq]
(Submitter supplied) We demonstrate that PTEN interacts with the transcription machinery. Using ChIP-seq, we show that PTEN co-localizes with RNAPII and binds to chromatin in promoter and putative enhancer regions. We further show that loss of PTEN affects RNAPII occupancy in gene bodies and correlates with gene expression changes. Loss of PTEN also increased cells’ sensitivity to transcription inhibition via small molecules.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 24 Samples
FTP download: GEO (BW, CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120439/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA493122
Series		Accession: GSE120439	ID: 200120439

767. Single cell gene expression profiling in normal HSCs and CML stem cells
(Submitter supplied) CML stem cells (CMLSCs) and normal hematopoietic stem cells (HSCs) display the same set of surface markers (CD34+CD38-CD90+CD45RA-), making it infeasible to separate these two populations within the same sample. To overcome this challenge, and to minimize variations in gene expression due to individual variation, here we perform single-cell RNA-seq to compare expression profiles of CMLSCs and HSCs isolated from the same patient. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 288 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81730/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322448
Series		Accession: GSE81730	ID: 200081730

768. Spatial control of oxygen delivery to 3D cultures alters cancer cell growth and gene expression
(Submitter supplied) Commonly used monolayer cell cultures lack the capacity to provide a physiologically relevant environment for cell culture in terms of cell-cell architecture, extracellular matrix composition, and spatiotemporal delivery of key growth factors and small molecules, such as oxygen. Here, we describe a three-dimensional (3D) approach to cell culture in vitro, utilizing a bioreactor system designed to control oxygenation of 3D cancer cell cultures, in order to better mimic tumor microenvironments observed in vivo. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 58 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129111/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA530150
Series		Accession: GSE129111	ID: 200129111

769. Variability in the Analgesic Response to Ibuprofen Following Third Molar Extraction is Associated with Differences in Activation of the Cyclooxygenase Pathway
(Submitter supplied) It has long been recognized that there is substantial inter-individual variability in the analgesic efficacy of non-steroidal anti-inflammatory drugs (NSAIDs), but the mechanisms underlying this variability are not well understood.  In order to characterize the factors associated with heterogeneity in response to ibuprofen, we performed functional neuroimaging, pharmacokinetic/pharmacodynamic assessments, biochemical assays, and gene expression analysis in twenty-nine healthy subjects who underwent third molar extraction. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 77 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120596/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA493653
Series		Accession: GSE120596	ID: 200120596

770. NOTCH signaling is activated in and contributes to resistance in enzalutamide-resistant prostate cancer cells
(Submitter supplied) Prostate cancer is the second leading cause of cancer death among men in the United States. The Androgen receptor (AR) antagonist Enzalutamide is a FDA approved therapy for treatment of late stage prostate cancer patients and is currently under clinical study for early stage prostate cancer treatment. After a short positive response period, patients will develop drug resistance. In this study we used RNA-sequencing and bioinformatics analysis to identify Notch signaling pathway as a deregulated pathway in Enzalutamide-resistant cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123379/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA508536
Series		Accession: GSE123379	ID: 200123379

771. RNA-seq of MDA-MB-231 siCt and siAXL
(Submitter supplied) Triple-Negative breast cancer (TNBC) is an aggressive subtype of breast cancer that is associated with poor prognosis due to its propensity to form metastases. Unfortunately, the current treatment options are limited to chemotherapy such that identification of actionable targets are needed. The receptor tyrosine kinase AXL plays a role in the tumor cell dissemination and its expression in TNBC correlates with poor patients? survival. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120268/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA492335
Series		Accession: GSE120268	ID: 200120268

772. Gene expression profiling of LNCaP cells following shRNA-mediated knockdown of TMEFF2 and growth in presence and absence of dihydrotestosterone
(Submitter supplied) TMEFF2 is an androgen regulated transmembrane protein mainly restricted to brain and prostate, that functions as a tumor suppressor in prostate cancer (PCa). Studies using publically available prostate cancer (PCa) datasets, reveal changes in the expression of TMEFF2 with disease stage, supporting an important role of TMEFF2 in this disease. However, the role of TMEFF2 in the biology and pathogenesis of PCa is still unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117180/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481362
Series		Accession: GSE117180	ID: 200117180

773. Bromodomain and extraterminal proteins foster the core transcriptional regulatory programs and confer vulnerability in liposarcoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 41 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111254/
Series		Accession: GSE111254	ID: 200111254

774. Bromodomain and extraterminal proteins foster the core transcriptional regulatory programs and confer vulnerability in liposarcoma (RNA-Seq)
(Submitter supplied) Purpose: Identification of core transcriptional regulatory programs and bromodomain and extraterminal (BET) protein dependency in liposarcoma (LPS)  Methods: ChIP-seq and RNA-seq were performed on LPS cells. Antibodies against H3K27ac, H3K4me1, H3K4me3, RNA-Pol2, BRD2, BRD3, BRD4, FOSL2, pan-RUNX, and DDIT3 (FUS-DDIT3) were used for ChIP-seq assays. The transcriptome responses of LPS141 and MLS402 cells to OTX015 and ARV-825 were compared. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111252/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436355
Series		Accession: GSE111252	ID: 200111252

775. Single-cell integrative analysis of CAR-T cell activation reveals a predominantly TH1/TH2 mixed response independent of differentiation
(Submitter supplied) We present the first comprehensive portrait of single-cell level transcriptional and cytokine signatures of anti-CD19 4-1BB/CD28/CD3ζ CAR-T cells upon antigen-specific stimulation. Both CD4+ ‘helper’ and CD8+ cytotoxic CAR-T cells are equally effective in directly killing target tumor cells and their cytotoxic activity is associated with the elevation of a range of TH1 and TH2 signature cytokines (e.g., IFNγ, TNFα, IL5, and IL13), as confirmed by the expression of master transcription factors TBX21 (Tbet) and GATA-3. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129007/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529684
Series		Accession: GSE129007	ID: 200129007

776. Force expression LNK suppresses interferon Gamma signaling
(Submitter supplied) LNK (SH2B3) is a key negative regulator of JAK-STAT signaling which has been extensively studied in malignant hematopoietic diseases. We found that LNK is significantly elevated in cutaneous melanoma; this elevation is correlated with hyperactive signaling of the RAS-RAF-MEK pathway. Elevated LNK enhances cell growth and survival in adverse conditions. Forced expression of LNK inhibits signaling by interferon-STAT1 and suppresses interferon (IFN) induced cell cycle arrest and cell apoptosis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 4 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127764/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA525355
Series		Accession: GSE127764	ID: 200127764

777. Transcriptome analysis of SH-SY5Y cells after knockdown of circSLC45A4
(Submitter supplied) We perturbed the expression levels of circSLC45A4 in the human neuroblastoma cell line (SH-SY5Y) by RNAi/siRNAs. 96 h post-knockdown the cells were harvested, RNA extracted with Trizol and polyA+ libraries were generated with Illumina's TruSeq RNA Library Prep Kit v2. We find many significant changes in the transcriptomic profile after knockdown of circSLC45A4 and the induction of many genes connected to nervous system development, neuron projection development, synapse organization and cell adhesion.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124001/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510531
Series		Accession: GSE124001	ID: 200124001

778. Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures
(Submitter supplied) The human immune system consists of many specialized cell subsets that simultaneously carry out a diverse range of functions using overlapping pathways and signals. Subset-specific immune profiling can resolve immune activity in autoimmune disease, cancer immunity, and infectious disease that may not be discoverable or detectable in analyses of crude blood samples. Here, we present a low-input microfluidic system for sorting immune cells into subsets and profiling their cellular states by gene expression analysis using full-length RNA-seq. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21697 128 Samples
FTP download: GEO (MATRIX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120442/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA493077
Series		Accession: GSE120442	ID: 200120442

779. HDAC Inhibitor-Induced Acetylation of KRAS Confers A Pro-Oncogenic Effect Limiting Treatment Response in Colorectal Cancer
(Submitter supplied) The limited clinical utility of HDAC inhibitors for the treatment of colorectal cancer (CRC) has until now remained an unresolved conundrum. Our findings provide comprehensive mechanistic insight into the ineffectiveness that defines HDAC inhibitors as a monotherapy for CRC. We identified that inhibition of HDAC2 promotes the emergence of a super-oncogenic KRAS by inducing K5 acetylation that fosters a previously undiscovered electrostatic interaction with R67 conserved in RAF kinases. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 40 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108191/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422779
Series		Accession: GSE108191	ID: 200108191

780. Oxaliplatin resistance is enhanced by saracatinib via upregulation of ABCG1 and Wnt/β-catenin signaling in hepatocellular carcinoma
(Submitter supplied) Background:Oxaliplatin-resistant hepatocellular carcinoma (HCC) is associated with increased insulin-like growth factor 1 (IGF1) paracrine signaling, and the IGF1 receptor can be downregulated by inhibition of Src kinases. Therefore, we sought to determine whether Src inhibition and oxaliplatin treatment exerted synergistic effects on HCC cell lines. Methods: The antitumor effects of combined treatment with saracatinib and oxaliplatin on proliferation were evaluated in HCC cells as well as in saracatinib- and oxaliplatin-resistant HCC cell lines using cell viability assays, plate colony formation assays, and cell cycle distribution detection. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129071/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529896
Series		Accession: GSE129071	ID: 200129071

781. Genome-wide maps of chromatin state and mRNA expression patterns in leukemic cell lines
(Submitter supplied) ATACseq and RNAseq were performed on a panel of leukemia cell lines of both B and T cell origin
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL20301 14 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129066/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529894
Series		Accession: GSE129066	ID: 200129066

782. Phenotypic variation between stromal cells differentially impacts engineered cardiac tissue function
(Submitter supplied) Understanding the relationship between parenchymal and supporting cell populations is paramount to recapitulate the multicellular complexity of native tissues. Incorporation of stromal cells is widely recognized to be necessary for the stable formation of stem cell-derived cardiac tissues, yet the types of stromal cells used has varied widely. This study systematically characterized several stromal populations and found that stromal phenotype and morphology was highly variable depending on cell source and exerted differential impacts on cardiac tissue function and iPSC-CM phenotype. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 22 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129058/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529887
Series		Accession: GSE129058	ID: 200129058

783. Gene are regulated by Myocardin
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129023/
Series		Accession: GSE129023	ID: 200129023

784. Transcriptome profiling  (RNA-seq) of wild type and MYOCD overexpression in human lung cancer cell line A549.
(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) of wild type and MYOCD overexpression in human lung cancer cell line A549. Methods: mRNA profiles of wild type（WT） and MYOCD overexpression (MYOCD)  human lung cancer cell line A549 were generated by deep sequencing, using Illumina GAIIx. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128919/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529786
Series		Accession: GSE128919	ID: 200128919

785. Transcriptome profiling  (RNA-seq) of wild type and MYOCD Knockdown in human lung cancer cell line A549.
(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) of wild type and MYOCD Knockdown in human lung cancer cell line A549. Methods: mRNA profiles of wild type（WT） and Dox inducible MYOCD Knockdown (MYOCD−/−)  human lung cancer cell line A549 were generated by deep sequencing, using Illumina GAIIx. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128918/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529787
Series		Accession: GSE128918	ID: 200128918

786. Gene expression regulated by CSA and CSB in neuroblastoma cell line
(Submitter supplied) Mutations in the CSA and CSB genes are causative of Cockayne syndrome neurological disorder. Since the identification of the indispensable functions of these two proteins in transcription-coupled repair and restoring RNA synthesis following DNA damage, the paradoxical milder clinical spectrum in CS-A patients has been puzzling. In this study we compared the effect of a CSA and a CSB defect at the levels of the cell and the intact organism. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129002/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529668
Series		Accession: GSE129002	ID: 200129002

787. SNHG15 is a bifunctional MYC-regulated noncoding locus encoding a lncRNA that promotes cell proliferation, invasion and drug resistance in colorectal cancer by interacting with AIF
(Submitter supplied) Thousands of long noncoding RNAs (lncRNAs) are aberrantly expressed in various types of cancers, however our understanding of their role in the disease is still very limited.   We applied RNAseq analysis from patient-derived data with validation in independent cohort of patients. We followed these studies with gene regulation analysis as well as experimental dissection of the role of the identified lncRNA by multiple in vitro and in vivo methods. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128998/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529665
Series		Accession: GSE128998	ID: 200128998

788. Proteomics identifies a marker signature of MAPKi resistance in melanoma
(Submitter supplied) Combined proteomic and RNAseq analysis on 6 melanoma cell cultures reveals a signature for resistance to MAPKi resistance.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128915/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529368
Series		Accession: GSE128915	ID: 200128915

789. Transient stabilization, rather than inhibition of MYC amplifies extrinsic apoptosis and therapeutic responses in refractory B-cell lymphoma
(Submitter supplied) Identification of gene expression changes following inhibition of GSK-3 in Burkitt lymphoma
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126529/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA522272
Series		Accession: GSE126529	ID: 200126529

790. HOIL-1/RBCK1 promotes p53 degradation in Renal cancer cells
(Submitter supplied) We performed RBCK1 depletion in renal cancer cells along with RNA sequencing. The expression profiling showed p53 signaling as a potential RBCK1 target and the conclusions were also verified in clinical samples.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119864/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490504
Series		Accession: GSE119864	ID: 200119864

791. Acquisition of a hybrid E/M state is essential for tumorigenicity of basal breast cancer cells
(Submitter supplied) Using the recently described CD104+/CD44hi antigen combination we demonstrate that tumorigenicity depends on individual cells residing in a hybrid E/M state. Acquisition of this E/M hybrid state is facilitated by the differential expression of EMT- TFs, like Snail accompanied by the expression of adult stem-cell programs. Transition from the highly tumorigenic E/M state to a fully mesenchymal phenotype, achieved by constitutive ectopic expression of Zeb1, is sufficient to drive cells out of the E/M hybrid state into an extreme mesenchymal (xM) state, which is accompanied by a substantial loss of tumorigenicity and a switch from canonical to non-canonical Wnt signaling.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119149/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488269
Series		Accession: GSE119149	ID: 200119149

792. Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [3pDGE]
(Submitter supplied) In this study, we report the performance of one such technique denoted as sparse full length sequencing (SFL), a ribosomal RNA depletion-based RNA sequencing approach that allows for the simultaneous sequencing of 96 samples and higher.  We offer comparisons to well established single-sample techniques, including: full coverage Poly-A capture RNA-seq and microarray, as well as another low-cost highly multiplexed technique known as 3’ digital gene expression (3’ DGE). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 95 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118798/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486816
Series		Accession: GSE118798	ID: 200118798

793. Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [SFL]
(Submitter supplied) In this study, we report the performance of one such technique denoted as sparse full length sequencing (SFL), a ribosomal RNA depletion-based RNA sequencing approach that allows for the simultaneous sequencing of 96 samples and higher.  We offer comparisons to well established single-sample techniques, including: full coverage Poly-A capture RNA-seq and microarray, as well as another low-cost highly multiplexed technique known as 3’ digital gene expression (3’ DGE). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21697 95 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118797/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486817
Series		Accession: GSE118797	ID: 200118797

794. Tumor and stromal reaction under drug treatment in EUS-derived xenografts of human pancreatic adenocarcinoma
(Submitter supplied) BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is unique for its high stromal components play important role for tumor progression and therapeutic resistance. However, relevant preclinical models that recapitulate these tumor microenvironment are lacking and how the differences in the microenvironment affect cancer cell behavior are poorly understood. Here, we investigated the effects of tumor microenvironment on cancer cells behavior and therapeutic response. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL25431 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118197/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA484828
Series		Accession: GSE118197	ID: 200118197

795. Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets
(Submitter supplied) The roles of tumor-associated macrophages (TAMs) and circulating monocytes in human cancer are poorly understood. Here, we show that monocyte subpopulation distribution and transcriptomes are significantly altered by the presence of endometrial and breast cancer. Furthermore, TAMs from endometrial and breast cancers are transcriptionally distinct from monocytes and their respective tissue-resident macrophages. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 116 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117970/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483877
Series		Accession: GSE117970	ID: 200117970

796. Maturation of human telomerase RNA component from an extended precursor
(Submitter supplied) Here, we develop nascent RNAend-Seq, in which we isolate nascent RNA and sequence the 3' ends of RNA precursors. Using a pulse-chase experimental design, we follow extended precursors of the telomerase RNA component (hTR) and show that the mature telomerase RNA derives from these species with slow kinetics compared to other small non-coding RNAs. The human disease causing gene PARN further delays maturation of the hTR precursor in PARN- mutant cancer cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL15520 56 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117054/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480915
Series		Accession: GSE117054	ID: 200117054

797. A549 cells and MSR-A549 cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 20 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96781/
Series		Accession: GSE96781	ID: 200096781

798. mRNA expression profile of A549 cells and MSR-A549 cells with or without JQ1 treatment
(Submitter supplied) To establish effective multitargeted KRAS pathway therapy, we analyzed mediators of acquired resistance to chronic momelotinib and MEK inhibitor exposure in A549 cells. Since inhibitor resistance was completely reversible after drug withdrawal for several passages, suggesting epigenetic reprogramming, we investigated whole mRNA expression profiles in A549, momelotinib and selumetinib resistant (MSR)-A549 cells and MSR-A549 cells following drug withdrawal for 10 days. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96779/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379664
Series		Accession: GSE96779	ID: 200096779

799. C19ORF66 broadly escapes viral-induced endonuclease cleavage and restricts Kaposi’s Sarcoma Associated Herpesvirus (KSHV)
(Submitter supplied) We report the application of RNA-seq to identify the mRNA targets of 4 herpesviral endonucleases and uncovered a cluster of transcripts escaping degradation from all tested endonucleases.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 10 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128866/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA529180
Series		Accession: GSE128866	ID: 200128866

800. Protein Tyrosine Phosphatase Non-receptor 3 Acts as a Tumor Suppressor and Boosts TGF-b Signaling Independent of its Phosphatase Activity
(Submitter supplied) Transforming Growth Factor  b (TGF-b) controls a variety of cellular functions during development. Abnormal TGF-b responses are commonly found in human diseases such as cancer, suggesting that TGF-b signaling must be tightly regulated. Here we report that Protein Tyrosine Phosphatase Non-receptor 3 (PTPN3) profoundly potentiates TGF-b signaling independent of its phosphatase activity. PTPN3 stabilizes TGF-b type I receptor (TbRI) through attenuating the interaction between Smurf2 and TbRI. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 4 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127903/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA525769
Series		Accession: GSE127903	ID: 200127903

801. CAR T cell trogocytosis and cooperative killing   regulate tumour antigen escape
(Submitter supplied) Chimeric antigen receptors (CARs) are synthetic receptors for antigen that reprogram T cell specificity, function and persistence. Patient-derived CAR T cells have demonstrated remarkable efficacy against a range of B-cell malignancies, and early trial results suggest activity in multiple myeloma. Despite high complete response rates, relapses occur in a large fraction of patients, some of which are antigen-negative and others antigen-low. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 17 Samples
FTP download: GEO (TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126753/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA523212
Series		Accession: GSE126753	ID: 200126753

802. Expression profile of Lo19S state cells and MM.1S tumors
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123639/
Series		Accession: GSE123639	ID: 200123639

803. Expression profile of MM.1S tumors folloiwing treatment with bortezomib
(Submitter supplied) MM.1S orthotopic tumors were analyzed fro their gene expression upon tumor outgrowth. In contorl/bortezomib/elesclmol and combo treatments.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123637/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509438
Series		Accession: GSE123637	ID: 200123637

804. Nascent RNA Sequencing after NMYC activation in SH-EP MYCNER cells
(Submitter supplied) In order to distinguish transcription changes from RNA modification and post transcription changed, nascent RNA seq via metabolic labeling of freshly synthesized RNA was carried out using 4sU labeling/biotin purification.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113861/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454309
Series		Accession: GSE113861	ID: 200113861

805. Identification of two distinct pathways of human myelopoiesis.
(Submitter supplied) The myeloid innate immune system plays key roles in the defence against parasites and bacteria, and carries out essential functions during tissue homeostasis and repair. It consist of neutrophils, macrophages, eosinophils, basophils and mast cells. Myelopoietic dysfunction or deregulation underlies numerous pathologies, ranging from immune deficiencies and allergies to myeloproliferative disorders and myeloid leukemia. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 320 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113046/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA449859
Series		Accession: GSE113046	ID: 200113046

806. Stem cell-associated heterogeneity in Glioblastoma results from intrinsic tumor plasticity shaped by the microenvironment
(Submitter supplied) Cancer stem cells (CSCs) have been proposed to underlie the hierarchical organization of Glioblastoma (GBM) causing resistance to treatment, however the identity of CSCs in solid tumors remains largely elusive. Here we find that GBM cells expressing cell membrane CSC-associated markers do not represent a clonal entity defined by distinct functional properties and/or transcriptomic profiles, but rather a plastic state that most cancer cells can adopt. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128195/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA526715
Series		Accession: GSE128195	ID: 200128195

807. PolyA-sequencing in IMR-32 neuroblastoma cells with shRNA mediated depletion of CDK12, CDK13 or GFP.
(Submitter supplied) We performed RNA-seq analysis of polA transcripts in IMR-32 cells with shRNA-mediated depletion of CDK12 and CDK13 and GFP as a control
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 10 Samples
FTP download: GEO (BW, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122304/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA504553
Series		Accession: GSE122304	ID: 200122304

808. PolyA-sequencing in Kelly and Kelly E9R neuroblastoma cells treated with THZ531 or DMSO
(Submitter supplied) We performed RNA-seq analsysis of polA transcripts in Kelly and Kelly E9 resistant (E9R) cells treated with THZ531 for 6h and DMSO as a control
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (BW, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122303/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA504554
Series		Accession: GSE122303	ID: 200122303

809. A role for ZNF598 in post-transcriptional gene regulation
(Submitter supplied) Transcriptomic changes in U2OS cells upon depletion of the RNA-binding protein ZNF598 were analyzed in non-treated and IL-1 beta treated cells in comparison to control U2OS cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116126/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA477345
Series		Accession: GSE116126	ID: 200116126

810. Gene expression profiling in neuroblastoma cell lines treated with THZ531 or DMSO
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL16043 GPL18573 45 Samples
FTP download: GEO (BW, CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113314/
Series		Accession: GSE113314	ID: 200113314

811. Nascent RNA sequencing in IMR-32 cells treated with THZ531 or DMSO
(Submitter supplied) We performed RNA-seq analsysis of nascent transcripts obtained by 4sU labeling in IMR-32 cells treated with THZ531 for 30min and 2h and DMSO as a control
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113313/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450798
Series		Accession: GSE113313	ID: 200113313

812. PolyA-sequencing in IMR-32 cells treated with THZ531 or DMSO
(Submitter supplied) We performed RNA-seq analsysis of polA transcripts in IMR-32 cells treated with THZ531 for 2 and 6h and DMSO as a control
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (BW, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113312/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450797
Series		Accession: GSE113312	ID: 200113312

813. RNA sequencing of LNZ308 glioma cells treated under differential conditions including monotherapies, dual therapy and synergistic triple regimen employing γ-irradiation, temozolomide and oncolytic measles virus.
(Submitter supplied) The synergistic regimen CT-VT-RT triggers proinflammatory antiviral signalling with activation of apoptotic cascades resulting in tumor cell death.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 45 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111247/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436345
Series		Accession: GSE111247	ID: 200111247

814. TRIM59 promotes gliomagenesis by inhibiting TC45 dephosphorylation of STAT3
(Submitter supplied) Although the oncogenic signalings driven by amplification and mutations of EGF receptor (EGFR) gene play a major role in glioblastoma pathogenesis, the responsible downstream mechanisms remain less clear. Here we demonstrate that tripartite motif-containing protein 59 (TRIM59), acting as a new downstream effector of EGFR signaling, regulates STAT3 activation in glioblastoma. EGFR signaling leads to TRIM59 upregulation through SOX9 that results in enhancing TRIM59 interaction with STAT3 in nucleus, and inhibiting STAT3 association with TC45 (the nuclear form of T cell protein tyrosine phosphatase TC-PTP), thereby maintaining STAT3 phosphorylation and activation and promoting tumorigenesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106557/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417374
Series		Accession: GSE106557	ID: 200106557

815. Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma
(Submitter supplied) DNA and RNA were isolated from snap frozen primary tumor tissue (human and mouse), and DNA was isolated from matched normal tissue (region matched non-tumor tissue for human, tail section for mouse). A mouse leg was also injected with cardiotoxin to induce tissue damage was taken following sacrifice and was snap frozen, then processed for RNA isolation to serve as a mouse tissue-normal for RNA sequencing. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 3 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128766/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA528817
Series		Accession: GSE128766	ID: 200128766

816. Single-cell profiling of cutaneous T-cell lymphoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124899/
Series		Accession: GSE124899	ID: 200124899

817. Flura-seq identifies organ-specific adaptations in metastasis-initiating cells
(Submitter supplied) Metastasis-initiating cells dynamically adapt to the distinct microenvironments of different organs, but these early adaptations are poorly understood due to the limited sensitivity of in situ transcriptomics.  We developed fluorouracil-labeled RNA sequencing (Flura-seq) for in situ analysis with unprecedented sensitivity.  Flura-seq utilizes cytosine deaminase (CD) to convert fluorocytosine to fluorouracil, covalently labeling nascent RNA for purification and sequencing. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16512 GPL11154 27 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118937/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487361
Series		Accession: GSE118937	ID: 200118937

818. m6A-RIP-seq of mRNA in HeLa cells undergoing EMT
(Submitter supplied) We report the application of m6A-RIP-seq to indentify the m6A modifications variation in genes invovled in EMT. Briefly, total polyadenylated RNA was isolated from HeLa cells treated with or without 10 ng/ml TGF-β for 3 days by use of TRIZOL reagent followed the using of FastTrack MAGMaxi mRNA isolation kit (Invitrogen). RNA fragmentation, m6A-seq, and library preparation were performed according to instructions of manufacture and the previously published protocol (Wang et al., 2015). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 8 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112795/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448996
Series		Accession: GSE112795	ID: 200112795

819. RNA sequencing on LNCaP cells
(Submitter supplied) RNA sequencing on LNCaP cells was carried out to study how tunicamycin-induced gene expression is affected by knockdown of EIF2AK3 and ATF4.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 28 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108212/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422857
Series		Accession: GSE108212	ID: 200108212

820. Extracellular matrix (ECM) stiffness and collagen-1 (col-1) responsive genes in 3D cultured mammary epithelial cells
(Submitter supplied) We report the expression profiles of MCF10A cells encapsulated in hydrogels of varying stiffness and composition. Cells were encapsulated for 7 days in either 1.) soft alginate and reconstituted basement membrane (rBM), 2.) stiff alginate and rBM, 3,) soft col-1 and rBM, or 4.) stiff col-1. We find global gene expression changes in response to enhanced ECM stiffness, independent of expression changes in response to col-1 exposure. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102506/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397902
Series		Accession: GSE102506	ID: 200102506

821. In situ 10-cell RNA sequencing in tissue and tumor biopsy samples
(Submitter supplied) We combined the tissue preservation and single-cell resolution of laser capture with an improved preamplification procedure enabling RNA sequencing of 10 microdissected cells.  This in situ 10-cell RNA sequencing (10cRNA-seq) can exploit fluorescent reporters of cell type in genetically engineered mice and is compatible with freshly cryoembedded clinical biopsies from patients.   By using small pools of microdissected cells, 10cRNA-seq thus results in improved per-cell reliability and sensitivity beyond existing approaches for single-cell RNA sequencing (scRNA-seq). more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 168 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120261/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA492323
Series		Accession: GSE120261	ID: 200120261

822. Nuclear miCLIP and Nuclear NKAP iCLIP
(Submitter supplied) To identify m6A sites on endogenous nuclear RNAs, we performed miCLIP to identify m6A sites in PANC-1 cells. To identify NKAP binding sites on endogenous nuclear RNAs, we performed iCLIP for flag-tag NKAP to analyze the nuclear RNA binding with NKAP in the same cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 2 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116425/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA477937
Series		Accession: GSE116425	ID: 200116425

823. Modeling and characterization of the dynamic gene regulatory networks underlying cancer drug resistance based on time-course RNA-seq data
(Submitter supplied) Drug resistance is a major cause for the failure of cancer chemotherapy or targeted therapy. However, the molecular regulatory mechanisms controlling the dynamic evolvement of drug resistance remain poorly understood. Thus, it is important to develop methods for unraveling gene regulatory mechanisms underlying the resistance to specific drugs. We used glioma differentiation therapy as a realistic case and time-course RNA-seq to investigate the temporal gene expression changes in sensitive and resistant cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128722/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA528639
Series		Accession: GSE128722	ID: 200128722

824. Concurrent single cell RNA and targeted DNA sequencing on a microfluidics device allows high-throughput identification of transcriptome and genome alterations during the development of tyrosine kinase inhibitor resistance in EGFR-mutant lung cancer cells
(Submitter supplied) Within the clonal heterogeneity of a tumor, the co-measurement of both genomic and transcriptomic signatures in single cells is of fundamental importance to accurately assess how the genetic information, for instance a somatic mutation, is correlated with a transcriptomic and cancer-related phenotype. However, there is currently no microfluidics-based high-throughput assay available that allows this analysis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL15520 GPL18573 1090 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112274/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA445448
Series		Accession: GSE112274	ID: 200112274

825. Paired TCR and transcriptome analysis of single T cells characterizes clonally expanded human conventional and unconventional CD8+ T cells
(Submitter supplied) Purpose: Single cell RNAseq has revolutionized our understanding of the heterogeneity of immune system. The goal of this study is to characterize functions of Mycobacterium tuberculosis (Mtb) specific CD8+ T cell clones using single cell RNAseq Methods: PBMCs from Mtb exposed patients were stimulated ex vivo with Mtb lysate for 12 hours. Activated CD8+ T cells were selected and single cell sorted based on the upregulation of activation markers, including CD154 and CD137. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 921 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107646/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA420968
Series		Accession: GSE107646	ID: 200107646

826. Targeting IDH1 as a pro-senescent therapy in high-grade serous ovarian cancer
(Submitter supplied) We found that targeting IDH1 in HGSC induces senescence by altering the repressive histone landscape of E2F target genes
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128700/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA528523
Series		Accession: GSE128700	ID: 200128700

827. A NIK-SIX signaling axis controls inflammation by targeted silencing of noncanonical NF-κB
(Submitter supplied) The non-canonical NF-κB signaling cascade is essential for lymphoid organogenesis, B-cell maturation, osteoclast differentiation, and inflammation in mammals, whereas dysfunction of this system is associated with human diseases, including immunological disorders and cancer. While controlled expression of NF-κB Inducing Kinase (NIK) is the rate-limiting step in non-canonical NF-κB activation, mechanisms of inhibition remain largely unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 20 Samples
FTP download: GEO (FPKM_TRACKING, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126535/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA522280
Series		Accession: GSE126535	ID: 200126535

828. Single-cell profiling of cutaneous T-cell lymphoma reveals underlying heterogeneity predicting with disease progression.
(Submitter supplied) Cutaneous T cell lymphomas (CTCL), encompassing a spectrum of T-cell lymphoproliferative disorders involving the skin, have collectively increased in incidence over the last 40 years. Sézary syndrome (SS) is an aggressive form of CTCL characterized by significant presence of malignant cells in both the blood and skin. The guarded prognosis for SS reflects a lack of reliably effective therapy, due in part to an incomplete understanding of disease pathogenesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122703/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506054
Series		Accession: GSE122703	ID: 200122703

829. Gene expression analysis in U251 and U87 cells transduced with NANEP5 vector.
(Submitter supplied) NANEP5 is a heterologus repressor of NANOG, which consist of NANOG homeodomain and HES1 repressor domain. In this study we explore transcriptomes of glioblastoma cells expressing NANEP5 in order to reveal putative mediators of pro-tumorigenic NANOG function.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121092/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA495626
Series		Accession: GSE121092	ID: 200121092

830. CBFβ-MYH11 fusion blocks hematopoietic differentiation via repression of a GATA2 gene program
(Submitter supplied) The CBFβ-MYH11 fusion generated by inv(16) aberration is proposed to block normal myeloid differentiation, but whether this subtype of leukemia cells is poised for an unique cell lineage remains unclear. Here, we surveyed the functional consequences of CBFβ-MYH11 in inv(16) patient blasts and two inducible systems by multi-omics profiling. The primary inv(16) cells stay closer with megakaryocyte and erythrocyte lineages along the cell differentiation trajectory, and share common transcriptomic signatures and epigenetic determiners. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 17 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117138/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481263
Series		Accession: GSE117138	ID: 200117138

831. E-cadherin loss induces autocrine activation of oncogenic growth factor signalling in metastatic lobular breast cancer.
(Submitter supplied) Background: Despite the fact that loss of E-cadherin is causal to the development and progression of invasive lobular breast cancer (ILC), no targeted therapy is available to treat this major breast cancer subtype. This study is aimed at identifying clinically targetable pathways that are aberrantly active downstream of E-cadherin loss in ILC. Methods: Reverse-phase protein array (RPPA) analyses were performed in the context of E-cadherin loss using mouse and human breast cancer cells. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL13112 6 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81977/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA323547
Series		Accession: GSE81977	ID: 200081977

832. Transcriptional regulation of autophagy-lysosomal function in BRAF-driven melanoma progression and chemoresistance
(Submitter supplied) To Study the role of mutant Braf V600E and ERK dependent phosphorylation of TFEB in regulation of autophagy and lysosome biogenesis in the context of melanoma growth and metastasis, we used whole geneome RNA-seq to study role TFEB mediated  BRAFV600E autophagy regulation.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122614/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA505778
Series		Accession: GSE122614	ID: 200122614

833. Recruitment of BRCA1 limits MYCN-driven accumulation of stalled RNA Polymerase in neuroblastoma
(Submitter supplied) Deregulation of the MYCN gene drives the development of neuronal and neuroendocrine tumors and is often associated with a particularly poor prognosis. Here we show that activation of MYCN in human neuroblastoma cells induces promoter escape of RNAPII. If pause release of RNAPII fails, MYCN recruits the BRCA1 protein to promoter-proximal regions. Recruitment of BRCA1 prevents MYCN-dependent accumulation of stalled RNAPII and enhances transcriptional activation by MYCN. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL10999 GPL18573 109 Samples
FTP download: GEO (BEDGRAPH, BW, CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111905/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438512
Series		Accession: GSE111905	ID: 200111905

834. In vivo generation of post-infarct human cardiac muscle by laminin-promoted cardiovascular progenitors
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below and contains: bulk RNA-seq of two time series of a xeno-free human cardiomyocyte differentiation protocol starting from HS1001 and H1 hECSs until day 94 cardiomyocytes, single cell sequencing of cardiovascular progenitors (H1 and HS1001-derived cardiovascular progenitors at day 9 and 11) and bulk RNA-Seq of H1 hECSs that have been transferred to a LN-221 matrix. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 88 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100725/
Series		Accession: GSE100725	ID: 200100725

835. Tumor-associated Reactive Astrocytes Aid the Evolution of Immunosuppressive Environment in Glioblastoma
(Submitter supplied) The role of activated astrocytes in glioblastoma environment
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24106 40 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128536/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA528024
Series		Accession: GSE128536	ID: 200128536

836. Single-cell RNA-seq of human cardiovascular progenitor cells generated with a chemically defined, xeno-free laminin based differentiation protocol
(Submitter supplied) Regeneration of injured human heart muscle is limited and an unmet clinical need. There are no methods for the reproducible generation of clinical quality stem-cell-derived cardiovascular progenitors (CVPs). We identified laminin-221 (LN-221) as the most likely expressed cardiac laminin. We produced it as human recombinant protein, and showed that LN-221 promotes differentiation of pluripotent hESCs towards cardiomyocyte lineage and downregulates pluripotency and teratoma associated genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127955/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA525863
Series		Accession: GSE127955	ID: 200127955

837. KLF6-dependent transcription in renal cancer cells
(Submitter supplied) The PDGF and mTOR pathways are clinically relevant therapeutic targets in clear cell renal cell carcinoma (ccRCC), but the molecular mechanisms that lead to their activation has remained poorly understood. By chromatin and transcriptomic profiling and functional analysis we have identified Kruppel like factor 6 (KLF6), a transcription factor of the zinc-finger family, as a critical regulator of the PDGF-mTOR axis in ccRCC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115763/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475969
Series		Accession: GSE115763	ID: 200115763

838. Screening in Human Cardiac Organoids Identifies a Requirement for the Mevalonate Pathway in Cardiomyocyte Proliferation
(Submitter supplied) Purpose: Induction of endogenous proliferation is a promising strategy for cardiac regeneration. We find that GSK3 inhibition activates a cell cycle network whereas MST1 inhibition drives the mevalonate pathway, with synergistic activation of proliferation. However, all GSK3 inhibitors tested also reduce contractile force in hCO. We screened for small molecule activators of cardiomyocyte proliferation that did not alter contractile force in hCOs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 14 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111853/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438501
Series		Accession: GSE111853	ID: 200111853

839. RNA-sequencing and swarm intelligence-enhanced classification algorithm development for blood-based disease diagnostics using spliced blood platelet RNA
(Submitter supplied) We report RNA-sequencing data of 80 tumor-educated blood platelet (TEP) samples isolated from 39 patients with lower-grade glioma (LGG) and 41 healthy donors (HD). This dataset can be employed as input for the thromboSeq source code (available via GitHub: https://github.com/MyronBest/) to reproduce the thromboSeq drylab pipeline.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 80 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107868/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA421730
Series		Accession: GSE107868	ID: 200107868

840. BET Bromodomain Inhibition Blocks the Function of a Critical AR-Independent Master Regulator Network in Lethal Prostate Cancer
(Submitter supplied) BET bromodomain inhibitors are known to block prostate cancer cell survival through suppression of c-Myc and androgen receptor (AR) function. However, little is known about other transcriptional modulators whose function is blocked by these drugs and the anti-tumor activity of BET bromodomain inhibition in AR-independent castration-resistant prostate cancers (CRPC), whose frequency may be increasing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 34 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98069/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA383856
Series		Accession: GSE98069	ID: 200098069

841. Gene expression analysis of previously treated hormone receptor-positive metastatic breast cancer
(Submitter supplied) A large-panel gene expression analysis was conducted to identify biomarkers associated with the effectiveness of adding palbociclib to fulvestrant
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 302 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128500/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA527860
Series		Accession: GSE128500	ID: 200128500

842. Genome-wide profile of cJun and p27 and gene expression profile in breast cancer cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 39 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112446/
Series		Accession: GSE112446	ID: 200112446

843. Gene expression profile in breast cancer cells
(Submitter supplied) We report the gene expression patterns in MDA-MB-231 (a line selected for low metastatic ability), MDA-MB-231-1833 (its bone-tropic metastatic derivative line), MDA-MB-231p27CK-DD (a phosphomimetic cell line), MDA-MB-231-1833shp27 (p27 knockdown cell line), MDA-MB-231-1833PF1502 (PI3K inhibitor treatment). It shows that the gene expression pattern are regulated in a p27 phosphorylation-dependent manner.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112445/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA447896
Series		Accession: GSE112445	ID: 200112445

844. Reassessment of Exosome Composition
(Submitter supplied) RNA-Seq of cellular and extracellular samples from DKO-1 and Gli36 cell lines. The distribution of extracellular RNA between microvesicles, and crude small extracellular vesicular vesicles fractionated based on flotation density in ioxdixanol is distinct between the different extracellular compartments.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL11154 42 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125905/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA517926
Series		Accession: GSE125905	ID: 200125905

845. Inhibition of NF-κB-dependent signaling enhances sensitivity and overcomes resistance to BET inhibition in uveal melanoma
(Submitter supplied) Bromodomain and extra terminal protein inhibitors (BETi) are epigenetic therapies aimed to target dysregulated gene expression in cancer cells. Despite early success of BETi in a range of malignancies, the development of drug resistance may limit their clinical application. We evaluated the mechanisms of BETi resistance in uveal melanoma (UM), a disease with little treatment options, using two approaches: a high-throughput combinatorial drug screen with the clinical BET inhibitor PLX51107, and RNA sequencing of BETi-resistant cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 54 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124059/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510635
Series		Accession: GSE124059	ID: 200124059

846. CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [RNA-Seq]
(Submitter supplied) Glioblastoma is an incurable brain cancer characterized by high genetic and pathological heterogeneity. Here we mapped active chromatin landscapes with gene expression, whole-exomes, copy number profiles, and DNA methylomes across 44 glioblastoma stem cell (GSCs) models, 50 primary glioblastomas, and 10 neural stem cells (NSCs) with the goal of identifying essential super enhancer (SE)-associated genes and the core transcription factors that establish them and glioblastoma identity. Glioblastomas segregate with two dominant enhancer profiles that coopt unique developmental transcription factor regulatory programs to enforce tumor identity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 98 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119834/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490436
Series		Accession: GSE119834	ID: 200119834

847. CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL23976 384 Samples
FTP download: GEO (BEDGRAPH, IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119776/
Series		Accession: GSE119776	ID: 200119776

848. H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo
(Submitter supplied) Xenografts from human pediatric brainstem gliomas bearing K27M in H3F3A were transduced with non silencing or H3F3A shRNA to assess the impact of the K27M on tumor growth, gene expression and epigenetics
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 130 Samples
FTP download: GEO (BED, BW, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115875/
Series		Accession: GSE115875	ID: 200115875

849. H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo [RNA-Seq]
(Submitter supplied) xenografts from human pediatric brainstem gliomas bearing K27M in H3F3A were transduced with non silencing or H3F3A shRNA to assess the impact of the K27M on tumor growth, gene expression and epigenetics
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL16791 50 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115873/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476347
Series		Accession: GSE115873	ID: 200115873

850. Identification of Functional Lung Adenocarcinoma Susceptibility Loci through Positional Integration with Human Alveolar Cell Epigenomes
(Submitter supplied) Lung adenocarcinoma (LUAD) is the predominant lung cancer subtype. To date, 15 single nucleotide polymorphisms (SNPs) have been reproducibly associated with LUAD susceptibility. However, as most SNPs identified in genome-wide association studies (GWAS) are not located in the coding regions of genes and are co-inherited with hundreds of SNPs in linkage disequilibrium (LD), mechanistic links to disease outcomes remain largely unexplored. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84273/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328496
Series		Accession: GSE84273	ID: 200084273

851. Genome-wide analyses of chromatin state in human mast cells reveal molecular drivers and mediators of allergic and inflammatory diseases
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 39 Samples
FTP download: GEO (TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125931/
Series		Accession: GSE125931	ID: 200125931

852. Transcriptomic profiling of human peripheral blood-derived mast cells
(Submitter supplied) Here, we characterized the transcriptome of MCs under steady state, immunoglobulin E (IgE)-sensitized and anti-IgE-treated conditions.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125887/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA517886
Series		Accession: GSE125887	ID: 200125887

853. Bone marrow-derived and dental pulp-derived human mesenchymal stem cell RNA-Seq
(Submitter supplied) Lineage commitment and tumorigenesis specify adult stem cells from different tissues or organs. To gain insight into the mechanism of this programming, phenotypic, functional and transcriptome analyses were performed in mesenchymal stem cells derived from human dental pulp (DPSCs) and bone marrow (BMSCs). DPSCs and BMSCs had similar morphologies and flow cytometric profiles, and were capable of tri-lineage differentiation into osteoblast, adipocyte and chondocyte. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE105nnn/GSE105145/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414958
Series		Accession: GSE105145	ID: 200105145

854. CD8+ T cells regulate tumor ferroptosis during cancer immunotherapy
(Submitter supplied) CD8+ T cells activated by cancer immunotherapy execute tumor clearance mainly by inducing cell death through perforin-granzyme- and Fas/Fas ligand-pathways. Ferroptosis is a form of cell death that differs from apoptosis and results from iron-dependent lipid peroxide accumulation. Although it was mechanistically illuminated in vitro, emerging evidence has shown that ferroptosis may be implicated in a variety of pathological scenarios. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128392/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA527311
Series		Accession: GSE128392	ID: 200128392

855. Inhibition of DOT1L and PRMT5 promote synergistic anti-tumor activity in a human MLL leukemia model induced by CRISPR/Cas9
(Submitter supplied) Previous studies have identified frequent MLL-AF4 chromosomal translocation breakpoints in patients. Using CRISPRscan, we designed different sgRNAs recognizing patient-specific sequences in intron 11 of the MLL and exon 3 of the AF4 genes, respectively. Using plasmid- and virus-free delivery of sgRNAs with Cas9 protein, we nucleofected CD34+ target cells derived from human umbilical cord blood. Following nucleofection, the cells were maintained in liquid culture supplemented with cytokines and chemokines optimized for growth of MLLr cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128342/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA527203
Series		Accession: GSE128342	ID: 200128342

856. RNA-seq of RKO cells with cTAZ KO or putback
(Submitter supplied) RKO cells with cTAZ KO or putback were subjected to RNA isolation and RNA-seq analyses were generated by deep sequencing using Illumina Hiseq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128257/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA526896
Series		Accession: GSE128257	ID: 200128257

857. scRNA-seq of pediatric glioblastoma patient-derived xenografts
(Submitter supplied) scRNA-seq of patient-derived xenografts.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (H5) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117599/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482625
Series		Accession: GSE117599	ID: 200117599

858. BRD9 defines a novel SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors [RNA-seq 2]
(Submitter supplied) Bromodomain-containing protein 9 (BRD9) was recently identified to be associated with the chromatin remodeling SWI/SNF(BAF) complex, yet its function within the complex has remained unclear. Here, using genome-scale CRISPR-Cas9 screens, we found that BRD9 constitutes a specific vulnerability in highly malignant pediatric rhabdoid tumors, which are driven by inactivating mutations of SMARCB1 subunit of SWI/SNF complexes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125775/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA517485
Series		Accession: GSE125775	ID: 200125775

859. Glucocorticoids Promote Breast Cancer Metastasis
(Submitter supplied) Next Generation Sequencing was applied to investigate the heterogeneity between tumors and distant metastases in different models of Breast Cancer cell lines and primary-derived xenografts. Global transcriptional profiling of the primary tumor and matched distant metastases (lung, liver, spleen) as well as circulating tumor cells (CTCs) allowed to identify glucocorticoid signalling as a mediator of metastasis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 41 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124817/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA513860
Series		Accession: GSE124817	ID: 200124817

860. Transcriptomic analysis of the interaction of choriocarcinoma spheroids with receptive vs. non-receptive endometrial epithelium cell lines: an in vitro model for human implantation
(Submitter supplied) The aim of this study was to establish an in vitro model to investigate the initial stages of human implantation based on co-culture of a) immortalized cells representing the receptive (Ishikawa) or non-receptive (HEC-1-A) endometrial epithelium with b) spheroids of a trophoblastic cell line (JEG-3) modified to express green fluorescent protein. After co-culturing Ishikawa cells with trophoblast spheroids, 310 and 298 genes increased or decreased their expression compared to non-co-cultured Ishikawa control cells, respectively; only 9 genes (5 increased and 4 decreased) were differentially expressed in HEC-1-A upon co-culture with trophoblast spheroids. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 21 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121790/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA498451
Series		Accession: GSE121790	ID: 200121790

861. BRD9 defines a novel SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 31 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120235/
Series		Accession: GSE120235	ID: 200120235

862. BRD9 defines a novel SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors [RNA-seq]
(Submitter supplied) Bromodomain-containing protein 9 (BRD9) was recently identified to be associated with the chromatin remodeling SWI/SNF(BAF) complex, yet its function within the complex has remained unclear. Here, using genome-scale CRISPR-Cas9 screens, we found that BRD9 constitutes a specific vulnerability in highly malignant pediatric rhabdoid tumors, which are driven by inactivating mutations of SMARCB1 subunit of SWI/SNF complexes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120233/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA492263
Series		Accession: GSE120233	ID: 200120233

863. Global transcriptional responses to KI-MS2-008 treatment and Myc inactivation via doxycycline addition
(Submitter supplied) The Myc/Max heterodimer has crucial roles in normal cellular processes such as cell proliferation, metabolism, apoptosis, and differentiation, but its activity is often deregulated in a majority of human cancers. In an effort to explore alternative modes of Myc perturbation, we identified KI-MS2-008 as a small molecule that binds Max and modulates Myc-driven transcription, and in some cellular contexts, KI-MS2-008 treatment leads to a decrease in c-Myc protein levels. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 64 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107222/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA419363
Series		Accession: GSE107222	ID: 200107222

864. CDKN2A-specific probe captured RNA-sequencing (RNACap-Seq) (HEK293T MCF7)
(Submitter supplied) The CDKN2A/B locus at 9p21.3 contains crucial tumor suppressors (P16, P14, and P15) and oncogenic lncRNA ANRIL genes. This locus is most frequently inactivated in cancer genomes by deletion and DNA methylation. However, the mechanisms coordinately regulating their expression level are far from clear. In the present study, a novel lncRNA, P14AS, was characterized in the antisense strand of the fragment near CDKN2A in human cell lines using CDKN2A-specific probe captured RNA-sequencing (RNACap-Seq).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128205/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA526737
Series		Accession: GSE128205	ID: 200128205

865. Next Generation Sequencing (RNA-Sequencing) for the analysis of RUNX3 targets in H460, H460-ERT2-RUNX3 WT and H460-ERT2-RUNX3 MT(K94/171R mutation)
(Submitter supplied) Purpose: The goal of this study is to compare the gene expression profiles of H460, H460-ERT2-RUNX3-WT and H460-ERT2-RUNX3-MT(K94/171R) cells. Methods: H460, H460-ERT2-RUNX3 WT, and H460-ERT2-RUNX3-MT(K94/171R) cells were serum-starved for 24 hr, and then stimulated with 10% serum or 10% serum + 1 uM 4-OHT for 0, 8, or 16 hr. RNA was extracted from the cells. Isolated total RNA was processed for preparation of an RNA-seq library using the Illumina TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA, USA). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128174/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA526672
Series		Accession: GSE128174	ID: 200128174

866. FET fusion oncoprotein-regulated genes in HT1080 cell line
(Submitter supplied) Some specific sarcomas and leukemias are defined by characteristic FET (FUS, EWSR1, TAF15) fusion oncogenes. Myxoid liposarcoma and Ewing sarcoma are the most common entities characterized by FUS-DDIT3 and EWSR1-FLI1, respectively. Here, we performed whole transcriptome analysis of HT1080 cells with either ectopic FUS-DDIT3 or ectopic EWSR1-FLI1 expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL22790 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125941/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA518039
Series		Accession: GSE125941	ID: 200125941

867. Single-Cell Transcriptome Analysis of CD34+ Stem Cell-Derived Myeloid Cells Infected With Human Cytomegalovirus
(Submitter supplied) Myeloid cells are important sites of lytic and latent infection by human cytomegalovirus (CMV). We previously showed that only a small subset of myeloid cells differentiated from CD34+ hematopoietic stem cells is permissive to CMV replication, underscoring the heterogeneous nature of these populations. The exact identity of susceptible and resistant cell types, and the cellular features characterizing permissive cells, however, could not be dissected using averaging transcriptional analysis tools such as microarrays and, hence, remained enigmatic. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 1 Sample
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124334/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA511666
Series		Accession: GSE124334	ID: 200124334

868. Fibroblast RNA-Seq data from three genodermatoses (RDEB, XPC and KS)
(Submitter supplied) Recessive dystrophic epidermolysis bullosa, Kindler syndrome and xeroderma pigmentosum C, are three cancer-prone genodermatoses whose causal genetic mutations cannot fully explain, on their own, the array of associated phenotypic manifestations. Recent evidence highlights the contributing role of the stromal microenvironment in the pathology of these disorders. To investigate common mechanisms that contribute to the pathogenic role played by dermal fibroblasts, we conducted a comparative gene expression analysis by RNA-Seq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119501/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489425
Series		Accession: GSE119501	ID: 200119501

869. Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity
(Submitter supplied) We discovered potent small molecule inhibitors against the WIN site of WDR5. These inhibitors selectively block the proliferation of mammalian cells carrying fusions of the MLL1 oncogene. Here, we show that these inhibitors result in the rapid displacement of WDR5 from chromatin in both sensitive (MV4:11) and non-sensitive (K562) cell lines, induce early changes in the distribution of active polymerases at a subset of WDR5-bound genes, and induce global transcript changes that are consistent with induction of the tumor suppressor p53.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL21290 GPL18573 GPL16791 77 Samples
FTP download: GEO (NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115377/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474736
Series		Accession: GSE115377	ID: 200115377

870. Whole transcriptome targeted gene quantification provides new insights on pulmonary sarcomatoid carcinomas
(Submitter supplied) Pulmonary sarcomatoid carcinomas (PSCs) are rare and aggressive histological types of non-small cell lung cancer (NSCLC) with a median overall survival of about 9-12 months. In detail, PSCs comprise five different histological subtypes: pleomorphic carcinoma (PLC), giant cell carcinoma (GCC), spindle cell carcinoma (SCC), carcinosarcoma (CS) and pulmonary blastoma (PB). Preoperative pathological diagnosis may fail to identify these tumors and therapeutic options are still limited. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110205/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433178
Series		Accession: GSE110205	ID: 200110205

871. Suppression of glioblastoma by a drug cocktail inducing tumor cells toward a neuronal fate
(Submitter supplied) Glioblastoma (GBM), the most common and aggressive malignant tumor in adult brain, is a notoriously fatal tumor. For many years, surgical resection and postoperative radiotherapy had been used for the treatment of GBM, which resulted in a poor median survival of about 12 months. Currently, Temozolomide (TMZ) as a clinically meaningful chemotherapy drug has become the standard first-line treatment for GBM, but with an increase of the median survival for about only 2.5 months. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110130/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432933
Series		Accession: GSE110130	ID: 200110130

872. Next Generation Sequencing Facilitates Quantitative Analysis of IFNα Stimulated Transcriptomes in HepG2, SETD2-KO, STAT1-KO and STAT1-K525ARe HepG2 cells
(Submitter supplied) Purpose: Using RNA-seq to analyze the different expressions induced by IFNα among the SETD2-KO HepG2 cells, STAT1-KO HepG2 cells and STAT1-K525A-Re HepG2 cells and HepG2 control cells Methods: mRNA profiles of HepG2 control cells and SETD2-KO cells, STAT1-KO cells, STAT1-K525A-Re cells were generated by deep sequencing, using BGISEQ-500RS. The sequence reads that passed quality filters were analyzed at the transcriptional level with RSEM (RNA-seq by Expectation Maximization).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98372/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384926
Series		Accession: GSE98372	ID: 200098372

873. Release of paused RNA-Polymerase II at specific introns and chromatin domains favors spontaneous DNA double strand break formation and predicts cancer translocations
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 28 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93040/
Series		Accession: GSE93040	ID: 200093040

874. Release of paused RNA-Polymerase II at specific introns and chromatin domains favors spontaneous DNA double strand break formation and predicts cancer translocations [RNA-seq]
(Submitter supplied) Transcriptional activation leads to transient accumulation of DNA Double Strand Breaks (DSBs), which might promote formation of chromosomal translocations. We report here the genomic distribution of DSBs in non-transformed mammary cells grown under unperturbed conditions, using genome-wide Breaks Labeling In Situ and Sequencing (BLISS). We found thousands of high-confidence DSBs, which were enriched at the promoters of a subset of moderately- to highly-transcribed genes (fragile promoters) and co-localized with Topoisomerase II beta. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93039/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA359573
Series		Accession: GSE93039	ID: 200093039

875. RNA sequencing analysis of selumetinib-resistant CRC cells lines
(Submitter supplied) RNA sequencing analysis to compare parental colorectal cancer cell lines and their selumetinib-resistant derivatives and identify expression changes and/or mutations that might contribute to resistance
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126109/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA521036
Series		Accession: GSE126109	ID: 200126109

876. Genome-wide identification of cancer-specific alternative splicing in circRNA
(Submitter supplied) Circular RNA (circRNA) is a group of RNA family generated by RNA circularization, which was discovered ubiquitously across different cancers. However, the internal structure of circRNA is hard to be determined since of the alternative splicing happened in exons and introns of circRNA and the cancer-specific alternative splicing of circRNA is less to be identified. Here we proposed a custom tool CircSplice, which could identify internal alternative splicing of circRNA and compare the differential splicing between samples. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124453/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512052
Series		Accession: GSE124453	ID: 200124453

877. The mSWI/SNF ATPase module mediates subcomplex identity and non-catalytic targeting in SCCOHT [RNA-seq]
(Submitter supplied) Perturbations to mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complexes have been widely implicated as driving events across cancers1. One such perturbation is the dual loss of the SMARCA4 and SMARCA2 ATPase subunits, which has recently been implicated in rare cancers such as small cell carcinoma of the ovary, hypercalcemic type (SCCOHT)2-5, SMARCA4-deficient thoracic sarcomas6 and dedifferentiated endometrial carcinomas7. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117311/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481742
Series		Accession: GSE117311	ID: 200117311

878. Risk SNPs mediated promoter-enhancer switching promotes prostate cancer progression through lncRNA PCAT19
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 12 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112164/
Series		Accession: GSE112164	ID: 200112164

879. Risk SNPs mediated promoter-enhancer switching promotes prostate cancer progression through lncRNA PCAT19 (RNA-seq data sets)
(Submitter supplied) To determine the functional mechanisms of PCAT19-long isoform and HNRNPAB, we conducted siRNA knockdown RNA-sequencing in prostate cancer cell line V16A.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106774/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417969
Series		Accession: GSE106774	ID: 200106774

880. Silencing SPIB in attached and floating state of H1703 lung cancer cells
(Submitter supplied) To gain mechanistic insight into the role of SPIB in anoikis resistance, we assessed the transcriptional profile of the genes involved using RNA sequencing
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106592/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417308
Series		Accession: GSE106592	ID: 200106592

881. Genome-wide maps in MCF-7 cells with six2 or CYP4Z1 3'UTR or CYP4Z2P 3'UTR overexpression or not
(Submitter supplied) Analysis of MCF-7 cells following  six2 or CYP4Z1 3'UTR or CYP4Z2P 3'UTR overexpression. Overexpression of six2 or CYP4Z1 3'UTR or CYP4Z2P 3'UTR positively regulates the abundance of embryonic stem cell function. Results provide insight into the role of six2 mediated-regulation on the ceRNA network between CYP4Z1 and pseudogene CYP4Z2P in breast cancer stemness.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116984/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480787
Series		Accession: GSE116984	ID: 200116984

882. Expression profiling by RNA-Seq of breast cancer samples from patients in walnut-consuming and control groups
(Submitter supplied) Consumption of walnuts has slowed breast cancer growth and/or reduced the risk of breast cancer in mice. The significantly reduced mean tumor size or numbers of tumors was associated with changing the expressions of many genes that are associated with cancer growth, survival and metastasis. Many women treated for breast cancer are interested in reducing the risk for recurrence. The study was a non-placebo, two-arm, clinical trial. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 21 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111073/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA435751
Series		Accession: GSE111073	ID: 200111073

883. Next Generation Sequencing Facilitates Quantitative Analysis of a circRNA, hsa_circ_0005505 regulated Transcriptomes in breast cancer cells (MDA-MB-231 lung metastatic cells LM2)
(Submitter supplied) Purpose: hsa_circ_0005505 stably knockdown cells (circ-sh1 and circ-sh2) and its corresponing control cells (con-sh) were constructed using its specific shRNAs. Next-generation sequencing (NGS) has used to examine hsa_circ_0005505 regulated transcripts. Methods:  mRNA profiles of circsh1, circsh2 and con-sh were generated by deep sequencing using IlluminaI HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111665/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA437772
Series		Accession: GSE111665	ID: 200111665

884. Oncogenic Antisense LncRNA P14AS Regulates Expression of ANRIL through AUF1 Binding
(Submitter supplied) The CDKN2A/B locus at 9p21.3 contains crucial tumor suppressor (P16, P14, and P15) and oncogenic lncRNA ANRIL genes. This locus is most frequently inactivated in cancer genomes by deletion and DNA methylation. However, the mechanisms coordinately regulating their expression level are far from clear. In the present study, a novel lncRNA, P14AS, was characterized in the antisense strand of the fragment near CDKN2A exon1 in human cell lines using CDKN2A-specific probe captured RNA-sequencing (RNACap-Seq).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127905/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA525771
Series		Accession: GSE127905	ID: 200127905

885. RNA-sequencing of fibrolamellar carcinoma (FLC) cell line treated with miR-375 mimic
(Submitter supplied) Fibrolamellar carcinoma (FLC) is a rare liver cancer. Expression of miR-375 is significantly lost in primary FLC tumors compared to non-malignant liver. Here, we treated a FLC cell line with miR-375 mimic or scramble control to determine the function of miR-375 in FLC.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125602/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516900
Series		Accession: GSE125602	ID: 200125602

886. Nucleotide excision repair capacity increases during differentiation of human embryonic carcinoma cells into neurons and muscle cells
(Submitter supplied) Embryonic stem cells can self-renew and differentiate, holding great promise for regenerative medicine. They also employ multiple mechanisms to preserve the integrity of their genomes. Nucleotide excision repair, a versatile repair mechanism, removes bulky DNA adducts from the genome. However, the dynamics of the capacity of nucleotide excision repair during stem cell differentiation remain unclear. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 14 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125370/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515931
Series		Accession: GSE125370	ID: 200125370

887. Next Generation Sequencing of Wild Type IFNG versus partial agonists in A549 cell line human transcriptomes
(Submitter supplied) Purpose: Next-generation sequencing (NGS) of human transcriptome of over 20,000 genes to compare gene expression of wild-type versus designed IFNG partial agonsits Methods: A549 cells were treated with either wild-type IFNG or partial agonists for 48 hours. RNA was extracted and prepared for NGS on using Thermo Ampliseq human transriptome kit on an Ion S5 XL system (Thermo). Relative expression was determined from the data. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24014 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122672/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA505995
Series		Accession: GSE122672	ID: 200122672

888. Transcriptome Analysis of PBMCs in peripheral blood of patients with hepatocellular carcinoma
(Submitter supplied) The aim of this study was to analyze the expression profile of circRNAs in PBMCs in peripheral blood of patients with hepatocellular carcinoma (HCC) by next-generation sequencing, and to identify potential markers for early diagnosis and prognosis of HCC, and to lay a foundation for further study on the mechanism of this molecule in PBMCs.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120663/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494021
Series		Accession: GSE120663	ID: 200120663

889. mRNA sequencing of single-cell and 20-cell pools of CD103+CD8+ and CD103-CD8+ T lymphocytes sorted from human ovarian cancer
(Submitter supplied) Cytotoxic T cells confer a prognostic benefit in many tumors, including ovarian cancer. We and others have previously identified a subset of CD8+ T cells, namely CD103+CD8+ T cells, that seems to have a better prognostic effect. The aim of this study is to identify how these CD103+ T cells differ from CD103-CD8+ T cells on mRNA level in human samples of ovarian cancer.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 120 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127888/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA525699
Series		Accession: GSE127888	ID: 200127888

890. CENPA-Bound Genes and Transcriptional Profiling of CENPA-Depleted Prostate Cancer Cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL20301 18 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127837/
Series		Accession: GSE127837	ID: 200127837

891. Transcriptional Profiling of CENPA-Depleted Prostate Cancer Cell Lines
(Submitter supplied) Overexpression of centromeric proteins has been identified in a number of human malignancies, though their functional and mechanistic contributions to disease progression have not been characterized. CENPA, the centromeric histone H3 variant, is the epigenetic mark that determines centromere identity. Here, we demonstrate that CENPA is highly overexpressed in prostate cancer in both tissue and cell lines, and the level of CENPA expression correlates with the stage of disease. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127836/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA525633
Series		Accession: GSE127836	ID: 200127836

892. ISL1-binding site
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 7 Samples
FTP download: GEO (BED, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122439/
Series		Accession: GSE122439	ID: 200122439

893. Next Generation Sequencing Facilitates Quantitative Analysis of ISL1 Regulated Transcriptomes
(Submitter supplied) The goals of this study are to analyze the transcriptome profiling (RNA-seq) after ISL1 overexpression in SGC7901.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122437/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA505256
Series		Accession: GSE122437	ID: 200122437

894. H3K4ox-Mediated Chromatin Condensation Protects Breast Cancer Cells from the DNA Damage Repair Machinery
(Submitter supplied) Using an H3K4ox-specific antibody, we determined that the H3K4ox modification is enriched in triple-negative breast cancer (TNBC) cells compared with luminal breast cancer subtypes—correlating with high LOXL2 levels— and, importantly, is found primarily in heterochromatin.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96064/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA378730
Series		Accession: GSE96064	ID: 200096064

895. Increased Serine and One Carbon Pathway Metabolism by PKCl/i Deficiency Promotes Neuroendocrine Prostate Cancer
(Submitter supplied) Increasingly effective therapies targeting the androgen receptor have paradoxically promoted the incidence of neuroendocrine prostate cancer (NEPC), the most lethal subtype of castration-resistant prostate cancer (PCa), for which there is no effective therapy. Here we report that protein kinase C (PKC)l/i is downregulated in de novo and during therapy-induced NEPC, which results in the upregulation of serine biosynthesis through an mTORC1/ATF4-driven pathway. more...
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL6244 GPL18573 19 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109763/
Series		Accession: GSE109763	ID: 200109763

896. Increased Serine and One Carbon Pathway Metabolism by PKCl/i Deficiency Promotes Neuroendocrine Prostate Cancer [RNA-seq]
(Submitter supplied) Increasingly effective therapies targeting the androgen receptor have paradoxically promoted the incidence of neuroendocrine prostate cancer (NEPC), the most lethal subtype of castration-resistant prostate cancer (PCa), for which there is no effective therapy. Here we report that protein kinase C (PKC)l/i is downregulated in de novo and during therapy-induced NEPC, which results in the upregulation of serine biosynthesis through an mTORC1/ATF4-driven pathway. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109752/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431975
Series		Accession: GSE109752	ID: 200109752

897. Bronchial premalignant lesions have distinct molecular subtypes associated with future histologic progression
(Submitter supplied) Exposure to cigarette smoke creates a field of injury throughout the entire respiratory tract inducing genomic alterations that lead to an “at-risk” airway where and lung cancers develop.  Lung squamous cell carcinoma (SCC) arises in the epithelial layer of the bronchial airways and is often preceded by the development of premalignant lesions(PMLs). The presence of high-grade persistent or progressive PMLs is a marker of increased lung cancer risk both at the lesion site elsewhere in the lung. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 448 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109743/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431899
Series		Accession: GSE109743	ID: 200109743

898. Distinct cancer-promoting stromal gene expression depending on lung function
(Submitter supplied) Chronic obstructive pulmonary disease (COPD) is an independent risk factor for lung cancer, but the underlying molecular mechanisms are unknown. We hypothesized that lung stromal cells activate pathological gene expression programs supporting oncogenesis. To identify molecular mechanisms operating in the lung stroma that support development of lung cancer. Study subjects included patients with- or without- lung cancer across a spectrum of lung function. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 64 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103404/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401720
Series		Accession: GSE103404	ID: 200103404

899. Polybrominated diphenyl ethers (PBDEs)
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119588/
Series		Accession: GSE119588	ID: 200119588

900. Effects of Polybrominated Diphenyl Ether (PBDE) Mixture on estrogen receptor positive (ER+) patient-derived tumor xenograft (PDX) model
(Submitter supplied) ER+ PDX (COH-SC31) were exposed to PBDE mixture for 1 weeks. RNA-sequencing analysis was performed to evalaute the gene expression changes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119587/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489668
Series		Accession: GSE119587	ID: 200119587

901. MicroRNA-mediated suppression of the TGF-β pathway confers transmissible and reversible CDK4/6 inhibitor resistance (RNA-Seq)
(Submitter supplied) CDK4/6 inhibition is now part of the standard armamentarium for patients with estrogen receptor (ER)-positive breast cancer, so that defining mechanisms of resistance is a pressing issue. Here, we identify increased CDK6 expression as a key determinant of acquired resistance after exposure to palbociclib in ER-positive breast cancer cells. Increased CDK6 in resistant cells was dependent on TGF-β pathway suppression via miR-432-5p expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117746/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483062
Series		Accession: GSE117746	ID: 200117746

902. RNA-Seq analysis of HIF-2a-responsive genes in clear-cell renal cell carcinoma
(Submitter supplied) We performed RNA-Seq analysis of wildtype and three EPAS1-/- 786-O single cell clones generated by CRISPR/Cas9 to identify the HIF-2a-responsive genes in this cell line. Samples from wildtype 786-O cells treated with DMSO or HIF-2a antagonist compound C2 were also included in this analysis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115389/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474756
Series		Accession: GSE115389	ID: 200115389

903. A Low-cost Multiplex Biomarker Assay Stratifies Colorectal Cancer Patient Samples into Clinically-relevant Subtypes
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL23782 GPL17586 GPL11154 159 Samples
FTP download: GEO (CEL, RCC, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101651/
Series		Accession: GSE101651	ID: 200101651

904. A Low-cost Multiplex Biomarker Assay Stratifies Colorectal Cancer Patient Samples into Clinically-relevant Subtypes: Singapore Cohort RNA-seq
(Submitter supplied) Objective: In order to personalise standard therapies based on molecular profiles, we previously classified colorectal cancers (CRCs) into five distinct subtypes (CRCAssigner) and later into four consensus molecular subtypes (CMS) with different prognoses and treatment responses. For clinical application, here we developed a low-cost multiplex biomarker assay.  Design: Three cohorts of primary (except one liver metastases) untreated and fresh frozen CRC samples (n=57) profiled by microarray and RNA-Seq were analyzed. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101588/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394898
Series		Accession: GSE101588	ID: 200101588

905. CRISPRi RNA-seq from K562 (ENCSR942XXL)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting HMBOX1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127169/
Series		Accession: GSE127169	ID: 200127169

906. CRISPRi RNA-seq from K562 (ENCSR911BML)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting ZC3H11A.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127168/
Series		Accession: GSE127168	ID: 200127168

907. CRISPRi RNA-seq from K562 (ENCSR905SEH)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting MITF.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127167/
Series		Accession: GSE127167	ID: 200127167

908. CRISPRi RNA-seq from K562 (ENCSR900AQL)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting KHSRP.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127166/
Series		Accession: GSE127166	ID: 200127166

909. CRISPRi RNA-seq from K562 (ENCSR898UNK)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting ARID3A.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127164/
Series		Accession: GSE127164	ID: 200127164

910. CRISPRi RNA-seq from K562 (ENCSR862UHT)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting DLX1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127163/
Series		Accession: GSE127163	ID: 200127163

911. CRISPRi RNA-seq from K562 (ENCSR850LOZ)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting GATA1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127162/
Series		Accession: GSE127162	ID: 200127162

912. siRNA RNA-seq from K562 (ENCSR820EGA)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting E2F6.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127160/
Series		Accession: GSE127160	ID: 200127160

913. CRISPRi RNA-seq from K562 (ENCSR819PCU)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting SETDB1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127159/
Series		Accession: GSE127159	ID: 200127159

914. CRISPRi RNA-seq from K562 (ENCSR810RIC)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting HOXB9.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127158/
Series		Accession: GSE127158	ID: 200127158

915. CRISPRi RNA-seq from K562 (ENCSR808HQN)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting NR2C2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127157/
Series		Accession: GSE127157	ID: 200127157

916. CRISPRi RNA-seq from K562 (ENCSR800PWS)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting TBL1XR1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127156/
Series		Accession: GSE127156	ID: 200127156

917. siRNA RNA-seq from MCF-7 (ENCSR783OQM)
(Submitter supplied) RNA-seq on CB-24 cells treated with siRNA targeting a non-specific control siRNA.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127155/
Series		Accession: GSE127155	ID: 200127155

918. CRISPRi RNA-seq from K562 (ENCSR781XJD)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting ZNF143.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127154/
Series		Accession: GSE127154	ID: 200127154

919. CRISPRi RNA-seq from K562 (ENCSR773VKE)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting FOXK2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127153/
Series		Accession: GSE127153	ID: 200127153

920. CRISPRi RNA-seq from K562 (ENCSR761AQZ)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference for a non-specific target (batch D control).  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127152/
Series		Accession: GSE127152	ID: 200127152

921. CRISPRi RNA-seq from K562 (ENCSR734VBC)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting HSF1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127151/
Series		Accession: GSE127151	ID: 200127151

922. CRISPRi RNA-seq from K562 (ENCSR733TFF)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting MEIS2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127150/
Series		Accession: GSE127150	ID: 200127150

923. CRISPRi RNA-seq from K562 (ENCSR733ROU)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting MAF1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127149/
Series		Accession: GSE127149	ID: 200127149

924. CRISPRi RNA-seq from K562 (ENCSR731XIE)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting TARDBP.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127148/
Series		Accession: GSE127148	ID: 200127148

925. CRISPRi RNA-seq from K562 (ENCSR731FEO)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting SMAD5.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127147/
Series		Accession: GSE127147	ID: 200127147

926. CRISPRi RNA-seq from K562 (ENCSR715EDZ)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting SP2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127145/
Series		Accession: GSE127145	ID: 200127145

927. CRISPRi RNA-seq from K562 (ENCSR713AEC)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting HINFP.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127141/
Series		Accession: GSE127141	ID: 200127141

928. CRISPRi RNA-seq from K562 (ENCSR701TVL)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting FOXM1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127138/
Series		Accession: GSE127138	ID: 200127138

929. CRISPRi RNA-seq from K562 (ENCSR688UTN)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting NR2F2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127137/
Series		Accession: GSE127137	ID: 200127137

930. siRNA RNA-seq from K562 (ENCSR669QED)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting LMNB2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127135/
Series		Accession: GSE127135	ID: 200127135

931. CRISPRi RNA-seq from K562 (ENCSR650QAK)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting SP1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127134/
Series		Accession: GSE127134	ID: 200127134

932. CRISPRi RNA-seq from K562 (ENCSR620DOP)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting KLF2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127133/
Series		Accession: GSE127133	ID: 200127133

933. CRISPRi RNA-seq from K562 (ENCSR619EYC)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting RFX5.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127132/
Series		Accession: GSE127132	ID: 200127132

934. CRISPRi RNA-seq from K562 (ENCSR608ORR)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting UBTF.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127131/
Series		Accession: GSE127131	ID: 200127131

935. CRISPRi RNA-seq from K562 (ENCSR591QYK)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting TRIM28.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127130/
Series		Accession: GSE127130	ID: 200127130

936. CRISPRi RNA-seq from K562 (ENCSR557BMX)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting GATA2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127129/
Series		Accession: GSE127129	ID: 200127129

937. CRISPRi RNA-seq from K562 (ENCSR552HTC)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting TFDP1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127128/
Series		Accession: GSE127128	ID: 200127128

938. CRISPRi RNA-seq from K562 (ENCSR550FIL)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting TEAD4.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127127/
Series		Accession: GSE127127	ID: 200127127

939. CRISPRi RNA-seq from K562 (ENCSR545HTM)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting USF1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127126/
Series		Accession: GSE127126	ID: 200127126

940. CRISPRi RNA-seq from K562 (ENCSR469EFL)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting STAT2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127125/
Series		Accession: GSE127125	ID: 200127125

941. CRISPRi RNA-seq from K562 (ENCSR409OFU)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting SNW1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127124/
Series		Accession: GSE127124	ID: 200127124

942. CRISPRi RNA-seq from K562 (ENCSR399QAP)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting TLE2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127123/
Series		Accession: GSE127123	ID: 200127123

943. CRISPRi RNA-seq from K562 (ENCSR389OCD)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting JUND.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127122/
Series		Accession: GSE127122	ID: 200127122

944. CRISPRi RNA-seq from K562 (ENCSR385ZTW)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting NFE2L1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127120/
Series		Accession: GSE127120	ID: 200127120

945. CRISPRi RNA-seq from K562 (ENCSR381TNV)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting NFATC1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127118/
Series		Accession: GSE127118	ID: 200127118

946. CRISPRi RNA-seq from K562 (ENCSR376CFR)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting STAT5A.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127115/
Series		Accession: GSE127115	ID: 200127115

947. CRISPRi RNA-seq from K562 (ENCSR369BHC)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting HDAC8.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127113/
Series		Accession: GSE127113	ID: 200127113

948. CRISPRi RNA-seq from K562 (ENCSR359VJC)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting HOXB4.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127112/
Series		Accession: GSE127112	ID: 200127112

949. CRISPRi RNA-seq from K562 (ENCSR357LVC)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting NR4A1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127111/
Series		Accession: GSE127111	ID: 200127111

950. siRNA RNA-seq from K562 (ENCSR301SWM)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting TCP1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127110/
Series		Accession: GSE127110	ID: 200127110

951. CRISPRi RNA-seq from K562 (ENCSR299HUJ)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting NRF1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127109/
Series		Accession: GSE127109	ID: 200127109

952. CRISPRi RNA-seq from K562 (ENCSR294ZCD)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting THAP1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127108/
Series		Accession: GSE127108	ID: 200127108

953. CRISPRi RNA-seq from K562 (ENCSR268DNJ)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting ERF.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127107/
Series		Accession: GSE127107	ID: 200127107

954. CRISPRi RNA-seq from K562 (ENCSR267BHU)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting ZNF395.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127105/
Series		Accession: GSE127105	ID: 200127105

955. CRISPRi RNA-seq from K562 (ENCSR263IOO)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting HMGB2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127104/
Series		Accession: GSE127104	ID: 200127104

956. siRNA RNA-seq from C4-2B (ENCSR244ZVP)
(Submitter supplied) RNA-seq on CB-24 cells treated with siRNA targeting ZFX.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127103/
Series		Accession: GSE127103	ID: 200127103

957. CRISPRi RNA-seq from K562 (ENCSR243VNX)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting HMGN2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127102/
Series		Accession: GSE127102	ID: 200127102

958. CRISPRi RNA-seq from K562 (ENCSR235ZEI)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting RBBP7.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127101/
Series		Accession: GSE127101	ID: 200127101

959. CRISPRi RNA-seq from K562 (ENCSR223QTD)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting ZBTB33.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127100/
Series		Accession: GSE127100	ID: 200127100

960. CRISPRi RNA-seq from K562 (ENCSR200UDS)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting CITED2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127099/
Series		Accession: GSE127099	ID: 200127099

961. CRISPRi RNA-seq from K562 (ENCSR190RZZ)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting BACH1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127098/
Series		Accession: GSE127098	ID: 200127098

962. CRISPRi RNA-seq from K562 (ENCSR184VVN)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting STAT1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127097/
Series		Accession: GSE127097	ID: 200127097

963. CRISPRi RNA-seq from K562 (ENCSR181WYS)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting WHSC1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127096/
Series		Accession: GSE127096	ID: 200127096

964. siRNA RNA-seq from K562 (ENCSR174FUO)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting STAT5A.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127095/
Series		Accession: GSE127095	ID: 200127095

965. CRISPRi RNA-seq from K562 (ENCSR171RTN)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting CTBP1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127094/
Series		Accession: GSE127094	ID: 200127094

966. CRISPRi RNA-seq from K562 (ENCSR171KMM)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting NFYB.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127093/
Series		Accession: GSE127093	ID: 200127093

967. CRISPRi RNA-seq from K562 (ENCSR160YSN)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting HMGN3.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127091/
Series		Accession: GSE127091	ID: 200127091

968. siRNA RNA-seq from C4-2B (ENCSR142YZV)
(Submitter supplied) RNA-seq on CB-24 cells treated with siRNA targeting a non-specific control siRNA.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127090/
Series		Accession: GSE127090	ID: 200127090

969. CRISPRi RNA-seq from K562 (ENCSR126GEQ)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting SMARCA4.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127089/
Series		Accession: GSE127089	ID: 200127089

970. CRISPRi RNA-seq from K562 (ENCSR123IMQ)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting ATF3.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127088/
Series		Accession: GSE127088	ID: 200127088

971. CRISPRi RNA-seq from K562 (ENCSR104QKG)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting SIX5.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127087/
Series		Accession: GSE127087	ID: 200127087

972. CRISPRi RNA-seq from K562 (ENCSR104JMN)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting MXD3.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127086/
Series		Accession: GSE127086	ID: 200127086

973. CRISPRi RNA-seq from K562 (ENCSR103URL)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting ZNF384.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127085/
Series		Accession: GSE127085	ID: 200127085

974. CRISPRi RNA-seq from K562 (ENCSR096VPS)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting NFYA.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127084/
Series		Accession: GSE127084	ID: 200127084

975. CRISPRi RNA-seq from K562 (ENCSR095PIC)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference for a non-specific target (batch E control).  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127083/
Series		Accession: GSE127083	ID: 200127083

976. CRISPRi RNA-seq from K562 (ENCSR084NTT)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting SRF.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127082/
Series		Accession: GSE127082	ID: 200127082

977. CRISPRi RNA-seq from K562 (ENCSR074FBG)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting TEAD2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127080/
Series		Accession: GSE127080	ID: 200127080

978. CRISPRi RNA-seq from K562 (ENCSR073QLQ)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting ILF2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127078/
Series		Accession: GSE127078	ID: 200127078

979. siRNA RNA-seq from K562 (ENCSR071JWS)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting LMNA.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127077/
Series		Accession: GSE127077	ID: 200127077

980. CRISPRi RNA-seq from K562 (ENCSR069OUL)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting HMGA1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127076/
Series		Accession: GSE127076	ID: 200127076

981. CRISPRi RNA-seq from K562 (ENCSR052ZPX)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting RELA.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127074/
Series		Accession: GSE127074	ID: 200127074

982. CRISPRi RNA-seq from K562 (ENCSR052BWT)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting USF2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127073/
Series		Accession: GSE127073	ID: 200127073

983. CRISPRi RNA-seq from K562 (ENCSR046FQX)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting LDB1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127071/
Series		Accession: GSE127071	ID: 200127071

984. CRISPRi RNA-seq from K562 (ENCSR043UMW)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting RNF2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127070/
Series		Accession: GSE127070	ID: 200127070

985. CRISPRi RNA-seq from K562 (ENCSR039VEQ)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting NONO.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127068/
Series		Accession: GSE127068	ID: 200127068

986. CRISPRi RNA-seq from K562 (ENCSR028FBD)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting DPF2.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127066/
Series		Accession: GSE127066	ID: 200127066

987. CRISPRi RNA-seq from K562 (ENCSR024HAR)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting STAT6.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127065/
Series		Accession: GSE127065	ID: 200127065

988. CRISPRi RNA-seq from K562 (ENCSR016WFQ)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference for a non-specific target (batch C control).  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127063/
Series		Accession: GSE127063	ID: 200127063

989. CRISPRi RNA-seq from K562 (ENCSR011GAO)
(Submitter supplied) RNA-seq on K562 cells treated by CRISPR interference targeting HMGN1.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127062/
Series		Accession: GSE127062	ID: 200127062

990. siRNA RNA-seq from MCF-7 (ENCSR005AHI)
(Submitter supplied) RNA-seq on MCF-7 cells treated with siRNA targeting ZFX.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127061/
Series		Accession: GSE127061	ID: 200127061

991. Gene expression profiles of 35 paired HCC and non-tumor tissues by RNA-seq data
(Submitter supplied) This study aims to uncover the transcriptomic variations in HCC
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 70 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124535/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512451
Series		Accession: GSE124535	ID: 200124535

992. Transcriptome of human keratinocytes with or without HPV16 oncogene expression
(Submitter supplied) We used freshly established immortalized human keratinocytes with a well-defined HPV16 E6 E7 expression cassette to get a more complete and less biased overview about global changes induced by HPV16 using RNA-seq. We identified novel factors regulated by HPV oncogenes that could serve an essential role in cancer development.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124357/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA511828
Series		Accession: GSE124357	ID: 200124357

993. Neurofibroma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (BW, TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118186/
Series		Accession: GSE118186	ID: 200118186

994. Differential expression in wild-type and mutant neurofibroma and MPNST cell lines
(Submitter supplied) Using RNA-seq we characterized gene expression changes occuring upon knockout of EZH2, EZH1, EZH1+EZH2 or SUZ12 in a neurofibroma cell line. We also investigated the transcriptional consequences of EZH1+EZH2 double knockout in a SUZ12-mutant MPNST cell line.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118185/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA484784
Series		Accession: GSE118185	ID: 200118185

995. Cellular gene expression during Hepatitis C Virus replication revealed by Ribosome profiling
(Submitter supplied) Background: Hepatitis C virus (HCV) infects human liver hepatocytes, often leading to liver cirrhosis and hepatocellular carcinoma (HCC). It is believed that chronic infection alters host gene expression and favours HCC development. In particular, HCV replication in Endoplasmic Reticulum (ER) derived membranes induces chronic ER stress. How HCV replication affects host mRNA translation and transcription at a genome wide level is not yet known. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127713/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA525090
Series		Accession: GSE127713	ID: 200127713

996. Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay
(Submitter supplied) Multi-modal single-cell assays provide high-resolution snapshots of complex cell populations but are mostly limited to transcriptome plus an additional modality. Here, we describe Expanded CRISPR-compatible Cellular Indexing of Transcriptomes and Epitopes by sequencing (ECCITE-seq) for the high-throughput characterization of at least five modalities of information from each single cell. We demonstrate application of ECCITE-seq to multimodal CRISPR screens with robust direct sgRNA capture and to clonotype-aware multimodal phenotyping of cancer samples.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL24676 GPL22245 GPL16791 24 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126310/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA521522
Series		Accession: GSE126310	ID: 200126310

997. Transcriptomic analysis of primary human T cells and murine RAW 264.7 macrophages 3D cultured in different collagen densities
(Submitter supplied) The density of the extracellular matrix has a dramatic impact on the gene expression profile of T cells and macrophages. This may reflect impaired immune response of T cells and macrophages in solid tumors.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18480 GPL18460 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124876/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA514057
Series		Accession: GSE124876	ID: 200124876

998. Structure and degradation of circular RNAs regulate PKR activation in innate immunity
(Submitter supplied) RNase L–mediated rapid degradation of circRNAs is required for PKR activation in innate immune responses and linked to the autoimmune disease systemic lupus erythematosus.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL18573 20 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122967/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA507020
Series		Accession: GSE122967	ID: 200122967

999. RNA-sequencing WT vs SOCS3 knockout Glioblastoma stem-cells
(Submitter supplied) Glioblastoma stem cells were infected with lentivirus expressing a non-targeting (gRNA-LacZ) or SOCS3 targeting gRNA to assess the function of SOCS3 in the stem cell compartment of Glioblastoma
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122486/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA505341
Series		Accession: GSE122486	ID: 200122486

1000. Targeting super-enhancer-driven oncogenic transcription by CDK7 inhibition in anaplastic thyroid cancer
(Submitter supplied) Anaplastic thyroid carcinoma (ATC) is one of the most aggressive malignancy and accounts for the majority of thyroid cancer-related deaths. Despite intensive research, there remains no effective treatment for patients with ATC. Here, we identify THZ1, a covalent inhibitor of cyclin-dependent kinase 7 (CDK7), as a potent anti-ATC compound by high-throughput chemical screening. ATC cells, but not papillary thyroid cancer (PTC) cells, are exceptionally sensitive to CDK7 inhibition. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL23227 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120177/
Series		Accession: GSE120177	ID: 200120177

