GEO DataSets

(Submitter supplied) Glioblastomas (GBMs) are highly aggressive, infiltrative, and heterogeneous brain tumors driven by complex driver mutations and glioma stem cells (GSCs). The neurodevelopmental transcription factors ASCL1 and OLIG2 are co-expressed in GBMs, but their role in regulating the heterogeneity and hierarchy of GBM tumor cells is unclear. Here, we show that oncogenic driver mutations lead to dysregulation of ASCL1 and OLIG2, which function redundantly to initiate brain tumor formation in a mouse model of GBM. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10999

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Colorectal cancer (CRC) progression from adenoma to adenocarcinoma is associated with global reduction in 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). DNA hypomethylation continues upon liver metastasis. Here we show that 5hmC is increased in metastatic liver tissue relative to the primary colon tumour and that expression of TET2 and TET3 is negatively correlated with risk for metastasis in patients with CRC. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL10999

18 Samples

Download data: NARROWPEAK

(Submitter supplied) In order to study the molecular mechanisms involving TCF4 in keratinocytes under different inflammatory responses, control and TCF4 knock down keratinocytes were stimulated with inflammatory cytokines and conducted RNA-seq to profile the gene expression.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

72 Samples

Download data: TXT

(Submitter supplied) We identified FOXM1 as an EAC-specific candidate transcription factor using GSEA analysis. Functionality of FOXM1 was evaluated in both EAC patient derived organoids and EAC cell lines by measuring cell proliferation, colony formation, and xenograft growth. A FOXM1 signature through the overlap of ESO26, SKGT4, and OE33 intersected ChIP-seq peaks and ESO26 siFOXM1 RNA-seq downregulated genes. Upstream transcriptional regulation of FOXM1 was evaluated with this FOXM1 gene signature and validated using pharmacological inhibition. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10999

6 Samples

Download data: NARROWPEAK, TXT

(Submitter supplied) Using methyl CpG binding domain capture and deep sequencing (MBD-seq) we examined white blood cells isolated from individuals with or without diabetic complications and non-diabetic controls. Sample where obatined from the Finnish Diabetic Nephropathy Study (FinnDiane)

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL10999

39 Samples

Download data: TXT

(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:

GPL10999 GPL24676

6 Samples

Download data: BED, TXT, XLSX

(Submitter supplied) Chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-Seq) was performed by using the anti-BPTF antibody in MGC803 cells to explore the downstream target genes of BPTF.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10999

4 Samples

Download data: BED, TXT

(Submitter supplied) We report the efficacy of androgen receptor inverse agonists (ARIAs) in altering androgen receptor (AR) transcriptional activity. Through RNA-sequencing studies in a panel of prostate cancer cell lines and patient derived xenograft models, we demonstrate ARIAs succcessfully inhibit androgen response gene sets. ChIP-seq and CUT&RUN studies demonstrate H3K27ac decreases at AR-target genes in response to treatment. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL24676 GPL10999 GPL9052

57 Samples

Download data: BED, HIC, TXT

(Submitter supplied) To investigate the downstream targets of the enhanced circHIPK3 expression accounting for high glucose-induced podocyte injury by RNA-seq

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

4 Samples

Download data: TXT

(Submitter supplied) Chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD) are clinically and molecularly heterogeneous diseases. We utilized clustering and integrative network analyses to elucidate roles for microRNAs (miRNAs) and miRNA isoforms (isomiRs) in COPD and ILD pathogenesis. Short RNA sequencing was performed on 351 lung tissue samples of COPD (n=145), ILD (n=144) and controls (n=64). more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL10999 GPL11154

371 Samples

Download data: TXT

(Submitter supplied) Small non-coding RNAs, in particular microRNAs (miRNAs), regulate fine-tuning of gene expression and can impact a wide range of biological processes. Using deep sequencing analysis, we investigated miRNA expression profiles in central and limbal regions of normal and diabetic human corneas. We identified differentially expressed miRNAs in limbus vs. central cornea in normal and diabetic (DM) corneas including both type I (T1DM/IDDM) and type II (T2DM/NIDDM). more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10999

44 Samples

Download data: TXT

(Submitter supplied) To investigate the differences in miRNA profiles, exosomal and cellular miRNA profiles between hCEp (Human Cervical Epithelia Cells) and Siha cells were generated by deep sequencing, in triplicate, using Illumina GAIIx. qRT–PCR validation was performed using TaqMan and SYBR Green assays

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10999

12 Samples

Download data: TXT

(Submitter supplied) RNA-sequencing for 6 samples

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

6 Samples

Download data: XLSX

(Submitter supplied) Background The role of ERG-status molecular subtyping in prognosis of prostate cancer (PCa) is still under debate. In this study, we identified differentially expressed genes (DEGs) according to ERG-status to explore their enriched pathways and implications in prognosis in Hispanic/Latino PCa patients. Methods RNA from 78 Hispanic PCa tissues from radical prostatectomies (RP) were used for RNA-sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL10999 GPL18573

95 Samples

Download data: TXT

(Submitter supplied) To investigate the underlying mechanism by which FAPα in HSCs promoted tumor cell EMT

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

6 Samples

Download data: TXT

(Submitter supplied) To define the global effects of tumor cell-derived FGFBP1 on the phenotype modifications of HSCs

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

6 Samples

Download data: XLS

(Submitter supplied) Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft-tissue sarcomas which lack effective drugs. Previous studies support the usefulness of MEK inhibitors (MEKis) for treating RAS-driven tumors, however, the lack of preclinical assessment of MEK inhibitors in MPNSTs limit the clinical application as well as the development of combination therapy. In this study, we comprehensively evaluated 8 MEK inhibitors in terms of efficiency, safety and mechanisms of resistance for treating MPNSTs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

12 Samples

Download data: TXT

(Submitter supplied) Abundantly expressed oncogenic miRNAs in endometrial cancer cells are identified by next-generation sequencing.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10999

2 Samples

Download data: CSV

(Submitter supplied) Whole exome sequencing and whole genome sequencing were performed using DNA isolated from MNKPL to identify genomic landscape. To investigate expression profiles of MNKPL, RNA sequencing (RNA-seq) was performed using RNA isolated from MNKPL. To clarify the origin and heterogeneity of MNKPL, single cell RNA-seq was conducted using leukemia cells of MNKPL and bone marrow mononuclear cells and CD34 positive bone marrow cells of a healthy donor.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

5 related Platforms

32 Samples

Download data: CSV, TXT, XLSX

(Submitter supplied) Mammalian RNA polymerase II (Pol II) initiation, elongation, termination and reinitiation are well studied, but how Pol II dynamically recycles after the transcription cycle remains unclear. By establishing in vitro and in vivo transcription recycling systems, we find that human Mediator 1 (MED1), when phosphorylated at the mammal-specific threonine 1032 by cyclin-dependent kinase 9, dynamically travels with Pol II throughout the transcribed genes to drive Pol II recycling. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

4 related Platforms

42 Samples

Download data: BIGWIG, BW, TXT