GEO DataSets

(Submitter supplied) The MYC oncogene encodes for the MYC protein and is frequently dysregulated across multiple cancer cell types, making it an attractive target for cancer therapy. MYC overexpression leads to MYC binding at active enhancers, resulting in a global transcriptional amplification of active genes. Since superenhancers are frequently dysregulated in cancer, we hypothesized that MYC preferentially invades into superenhancers and alters the cancer genome organization. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL15520 GPL16791 GPL25431

28 Samples

Download data: HIC, NARROWPEAK, TSV, TXT

(Submitter supplied) We propose that multiple CTCF sites on same motif orientation could cooperate with each other for stable enhancer-promoter interactions in the β-globin locus.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: BW

(Submitter supplied) Epstein-Barr virus (EBV) episome is known to interact with the three-dimensional structure of human genome in infected cells. However, the exact locations of these interactions and their potential functional consequences remain unclear. Recently the high-resolution chromatin interaction capture (Hi-C) assays in lymphoblastoid cells have become available enabling us to precisely map the contacts between the EBV episome(s) and the human host genome. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

2 Samples

Download data: BED

(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; Other

Platform:

GPL20795

74 Samples

Download data: BED, BEDGRAPH, CSV

(Submitter supplied) By CRISPR/Cas9 DNA-fragment editing, in conjunction with chromosome conformation capture, ChIP-seq and RNA-seq technology, we studied CRISPR single cell clones of duplicated CBS-containing enhancers or promoters in the Pcdhα gene cluster. We found that CTCF plays an essential role in determining promoter choice and enhancer selection. In addition, the choices mediated by CTCF is based on the chromatin loops formed between forward-reverse convergent CBS pairs with the proximal one dominant.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20795

11 Samples

Download data: BED

(Submitter supplied) By CRISPR/Cas9 DNA-fragment editing, in conjunction with chromosome conformation capture, ChIP-seq and RNA-seq technology, we studied CRISPR single cell clones of duplicated CBS-containing enhancers or promoters in the Pcdhα gene cluster. We found that CTCF plays an essential role in determining promoter choice and enhancer selection. In addition, the choices mediated by CTCF is based on the chromatin loops formed between forward-reverse convergent CBS pairs with the proximal one dominant.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

14 Samples

Download data: CSV

(Submitter supplied) By CRISPR/Cas9 DNA-fragment editing, in conjunction with chromosome conformation capture, ChIP-seq and RNA-seq technology, we studied CRISPR single cell clones of duplicated CBS-containing enhancers or promoters in the Pcdhα gene cluster. We found that CTCF plays an essential role in determining promoter choice and enhancer selection. In addition, the choices mediated by CTCF is based on the chromatin loops formed between forward-reverse convergent CBS pairs with the proximal one dominant.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20795

46 Samples

Download data: BEDGRAPH

(Submitter supplied) By CRISPR/Cas9 DNA-fragment editing, in conjunction with chromosome conformation capture, ChIP-seq and RNA-seq technology, we studied CRISPR single cell clones of duplicated CBS-containing enhancers or promoters in the Pcdhα gene cluster. We found that CTCF plays an essential role in determining promoter choice and enhancer selection. In addition, the choices mediated by CTCF is based on the chromatin loops formed between forward-reverse convergent CBS pairs with the proximal one dominant.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20795

3 Samples

Download data: BED

(Submitter supplied) We used RNA-Seq, ChIP-Seq, 4C-Seq and HiChIP to assess the role of MYC in the transcriptional repression induced by DHT in prostate cancer.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

3 Samples

Download data: TXT

(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; Other

Platforms:

GPL24676 GPL18573 GPL16791

47 Samples

Download data: TXT, WIG

(Submitter supplied) We used RNA-Seq, ChIP-Seq and 4C-Seq to assess the role of MYC in the transcriptional repression induced by DHT in prostate cancer.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

2 Samples

Download data: WIG

(Submitter supplied) We used RNA-Seq, ChIP-Seq and 4C-Seq to assess the role of MYC in the transcriptional repression induced by DHT in prostate cancer.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18573 GPL16791

14 Samples

Download data: TXT

(Submitter supplied) We used RNA-Seq, ChIP-Seq and 4C-Seq to assess the role of MYC in the transcriptional repression induced by DHT in prostate cancer.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL24676

28 Samples

Download data: TXT

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

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL13304

15 Samples

Download data: WIG

(Submitter supplied) In this study, we further characterized the hkCP and dCP enhancers, which were identified by STARR-seq, and shown to have an intrinsic capacity to interact with a specific type of core promoter depending on the presence of a DRE motif [9]. hkCP enhancers are marked by H3K4me3, associated with TAD borders, and mediate large TSS-clustered interactions to promote robust transcription. Furthermore, they contain the architectural proteins CAP-H2, Chromator, DREF and Z4. more...

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL13304

6 Samples

Download data: HIC, TXT

(Submitter supplied) In this study, we further characterized the hkCP and dCP enhancers, which were identified by STARR-seq, and shown to have an intrinsic capacity to interact with a specific type of core promoter depending on the presence of a DRE motif [9]. hkCP enhancers are marked by H3K4me3, associated with TAD borders, and mediate large TSS-clustered interactions to promote robust transcription. Furthermore, they contain the architectural proteins CAP-H2, Chromator, DREF and Z4. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

9 Samples

Download data: WIG

(Submitter supplied) Gene activity programmes in different cell types control development and homeostasis of multi-cellular organisms. Spatial genome organization controls gene activity by facilitating or restricting contacts between gene promoters and remote gene enhancers. Functionally related co-regulated genes are often located together in genomes loci. The spatial organization of very large co-regulated gene loci remains poorly understood. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

4 Samples

Download data: TXT

(Submitter supplied) Interactions between transcriptional promoters and their distal regulatory elements play an important role in transcriptional regulation; however, the extent to which these interactions are subject to rapid modulations in response to signals is unknown. Here, we use promoter capture Hi-C to demonstrate a rapid reorganization of promoter anchored chromatin loops within four hours after induction of differentiation of 3T3-L1 preadipocytes. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL18480

74 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) CCAT1-L is a highly expressed long noncoding RNA located in the colorectal cancer specific super enhance region about 500 kb upstream of MYC gene. Knockdown of CCAT1-L significantly down-regulated interaction frequency between CCAT1 and MYC locus and repress MYC expression, suggesting a long-range chromatin interaction between CCAT1-L and MYC locus maintained by CCAT1-L underlie the MYC regulation. To further validate this hypothesis, multiplexed 3C sequencing (3C-seq) was employed to evaluate chromatin interaction strength between CCAT1-L and MYC locus in CCAT1-L knockdown and scramble knockdown (Scr) HT29 cells.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

1 Sample

Download data: BEDGRAPH

(Submitter supplied) We have used RNA-seq to examine gene expression from paired human CRC/control mucosa samples and identified CRC-specific expressed long noncoding RNAs

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: BW