GEO DataSets

(Submitter supplied) Epigenetic mechanisms contribute to the initiation and development of cancer, and epigenetic variation promotes dynamic gene expression patterns that facilitate tumor evolution and adaptation. While the NCI-60 panel represents a diverse set of human cancer cell lines that has been used to screen chemical compounds, a comprehensive epigenomic atlas of these cells has been lacking. Here, we report an integrative analysis of 60 human cancer epigenomes, representing a catalog of activating and repressive histone modifications. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

540 Samples

Download data: BEDGRAPH, GRAPH

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Oryza sativa

Type:

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

Platform:

GPL24468

513 Samples

Download data: BW, TXT

(Submitter supplied) Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24468

4 Samples

Download data: BW

(Submitter supplied) Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. more...

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24468

38 Samples

Download data: BW

(Submitter supplied) Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24468

58 Samples

Download data: BW

(Submitter supplied) Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24468

58 Samples

Download data: TXT

(Submitter supplied) Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24468

355 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

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

Platform:

GPL21273

58 Samples

Download data: BW, TXT

(Submitter supplied) Activation of transcription enhancers, especially super enhancers, is one of the important epigenetic features of tumorigenesis. However, only very few studies reported how the enhancer landscape evolves during tumorigensis. Here we utilized a proteomics approach and found that H3K27ac and H4K8ac are elevated in the mammary tumor of MMTV-PyVT mouse model, which was then confirmed by IHC results in human BRCA chips. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21273

46 Samples

Download data: BW

(Submitter supplied) Activation of transcription enhancers, especially super enhancers, is one of the important epigenetic features of tumorigenesis. However, only very few studies reported how the enhancer landscape evolves during tumorigensis. Here we utilized a proteomics approach and found that H3K27ac and H4K8ac are elevated in the mammary tumor of MMTV-PyVT mouse model, which was then confirmed by IHC results in human BRCA chips. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

12 Samples

Download data: TXT

(Submitter supplied) Enhancer variation has been proposed as a major cause of cancer heterogeneity – however, mechanisms driving patient-specific enhancer cartographies remain unclear. Here we applied microscale histone modification profiling to delineate the landscape of enhancers in primary gastric adenocarcinoma, analyzing 132 epigenomic profiles of primary tumors, normal tissues, and cell lines

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

72 Samples

Download data: BW

(Submitter supplied) Multiple convergent pathways resulting in inhibition of the transcription factor EBF1 is a major cause of TERT upregulation.

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL20301

36 Samples

Download data: BW, TXT, XLS, XLSX

(Submitter supplied) Multiple convergent pathways resulting in inhibition of the transcription factor EBF1 is a major cause of TERT upregulation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

3 Samples

Download data: TXT

(Submitter supplied) Multiple convergent pathways resulting in inhibition of the transcription factor EBF1 is a major cause of TERT upregulation.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

16 Samples

Download data: TXT

(Submitter supplied) Multiple convergent pathways resulting in inhibition of the transcription factor EBF1 is a major cause of TERT upregulation.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL11154 GPL21290

6 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; Other; Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL21290 GPL11154

75 Samples

Download data: BW, NARROWPEAK, TXT, XLS, XLSX

(Submitter supplied) Multiple convergent pathways resulting in inhibition of the transcription factor EBF1 is a major cause of TERT upregulation.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

2 Samples

Download data: NARROWPEAK

(Submitter supplied) Multiple convergent pathways resulting in inhibition of the transcription factor EBF1 is a major cause of TERT upregulation.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21290

4 Samples

Download data: TXT

(Submitter supplied) Multiple convergent pathways resulting in inhibition of the transcription factor EBF1 is a major cause of TERT upregulation.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) Comprehensive downstream mapping of HNF4α revealed its role in regulating GC metabolism via regulation of IDH1

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL16791

23 Samples

Download data: TXT, XLS