GEO DataSets

(Submitter supplied) There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not depend on this structural protein. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

2 Samples

Download data: CLOUPE, CSV

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

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL13112 GPL16791 GPL17021

47 Samples

Download data: CLOUPE, CSV, TSV, WIG

(Submitter supplied) There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not depend on this structural protein. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

2 Samples

Download data: CSV

(Submitter supplied) There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not depend on this structural protein. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL17021 GPL16791

17 Samples

Download data: CSV

(Submitter supplied) There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not depend on this structural protein. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16791 GPL13112

4 Samples

Download data: WIG

(Submitter supplied) There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not depend on this structural protein. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: TSV

(Submitter supplied) There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not depend on this structural protein. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

18 Samples

Download data: WIG

(Submitter supplied) CTCF is an architectural protein with a critical role in connecting higher-order chromatin folding in pluripotent stem cells. Recent reports have suggested that CTCF binding is more dynamic during development than previously appreciated. Here we set out to understand the extent to which shifts in genome-wide CTCF occupancy contribute to the 3-D reconfiguration of fine-scale chromatin folding during early neural lineage commitment. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL19057

16 Samples

Download data: BED, NARROWPEAK, TXT

(Submitter supplied) Transcription factors (TFs) bind specific sequences in promoter-proximal and distal DNA elements in order to regulate gene transcription. RNA is transcribed from both promoter-proximal and distal DNA elements, and some DNA-binding TFs have also been shown to bind RNA. These obsevations led us to postulate that RNA transcribed from regulatory elements contributes to stable TF occupancy at these regulatory elements. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: WIG

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

Organism:

Mus musculus

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL13112

9 Samples

Download data: BED, BW, WIG

(Submitter supplied) Transcription factors (TFs) bind specific sequences in promoter-proximal and distal DNA elements in order to regulate gene transcription. RNA is transcribed from both promoter-proximal and distal DNA elements, and some DNA-binding TFs have also been shown to bind RNA. These obsevations led us to postulate that RNA transcribed from regulatory elements contributes to stable TF occupancy at these regulatory elements. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

3 Samples

Download data: BW, WIG

(Submitter supplied) Transcription factors (TFs) bind specific sequences in promoter-proximal and distal DNA elements in order to regulate gene transcription. RNA is transcribed from both promoter-proximal and distal DNA elements, and some DNA-binding TFs have also been shown to bind RNA. These obsevations led us to postulate that RNA transcribed from regulatory elements contributes to stable TF occupancy at these regulatory elements. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

4 Samples

Download data: BED, WIG

(Submitter supplied) Transcription factors (TFs) bind specific sequences in promoter-proximal and distal DNA elements in order to regulate gene transcription. RNA is transcribed from both promoter-proximal and distal DNA elements, and some DNA-binding TFs have also been shown to bind RNA. These obsevations led us to postulate that RNA transcribed from regulatory elements contributes to stable TF occupancy at these regulatory elements. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

19 Samples

Download data: WIG

(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) CCCTC binding factor (CTCF) is an important factor in the maintenance of chromatin chromatin interactions, yet the mechanism regulating its binding to chromatin is unknown. We demonstrate that zinc finger protein 143 (ZNF143) is a key regulator for CTCF bound promoter enhancer loops. In the murine genome, a large percentage of CTCF and ZNF143 DNA binding motifs are distributed 37 bp apart in the convergent orientation. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL19057 GPL21103

25 Samples

Download data: BW, HIC, TXT

(Submitter supplied) Although extended pluripotent stem cells (EPSCs) have the potential to form both embryonic and extraembryonic lineages, how their transcriptional regulatory mechanism differs from that of embryonic stem cells (ESCs) remains unclear. Here, we discovered that YY1 binds to specific open chromatin regions in EPSCs. Yy1 depletion in EPSCs leads to a gene expression pattern more similar to that of ESCs than control EPSCs. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL21273

63 Samples

Download data: BW, TAR, TXT