GEO DataSets

(Submitter supplied) Recent studies of genome-wide chromatin interactions have revealed that the human genome is partitioned into many self-associating topological domains. The boundary sequences are enriched for binding sites of CTCF and the cohesin complex, implicating these two factors in the establishment or maintenance of topological domains. To determine the role of cohesin and CTCF in higher order chromatin architecture in human cells, we proteolytically cleaved the cohesin complex from interphase chromatin and examined changes in chromosomal organization as well as transcriptome. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

18 Samples

Download data: BW, RPKM, TXT

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL19057 GPL16417 GPL17021

88 Samples

Download data: BW, WIG

(Submitter supplied) The genome is organized via CTCF/cohesin binding sites, which partition chromosomes into 1-5Mb topologically associated domains (TADs), and further into smaller contact sub-domains within TADs (sub-TADs; 40-1000kb). Here we examined in vivo an ~80kb sub-TAD, containing the mouse α-globin gene cluster, lying within a ~1Mb TAD. We find that the sub-TAD is flanked by predominantly convergent CTCF/cohesin sites which are ubiquitously bound by CTCF but only interact during erythropoiesis, defining a self-interacting erythroid compartment. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

9 Samples

Download data: WIG

(Submitter supplied) The genome is organized via CTCF/cohesin binding sites, which partition chromosomes into 1-5Mb topologically associated domains (TADs), and further into smaller contact sub-domains within TADs (sub-TADs; 40-1000kb). Here we examined in vivo an ~80kb sub-TAD, containing the mouse α-globin gene cluster, lying within a ~1Mb TAD. We find that the sub-TAD is flanked by predominantly convergent CTCF/cohesin sites which are ubiquitously bound by CTCF but only interact during erythropoiesis, defining a self-interacting erythroid compartment. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL17021

36 Samples

Download data: BW

(Submitter supplied) The genome is organized via CTCF/cohesin binding sites, which partition chromosomes into 1-5Mb topologically associated domains (TADs), and further into smaller contact sub-domains within TADs (sub-TADs; 40-1000kb). Here we examined in vivo an ~80kb sub-TAD, containing the mouse α-globin gene cluster, lying within a ~1Mb TAD. We find that the sub-TAD is flanked by predominantly convergent CTCF/cohesin sites which are ubiquitously bound by CTCF but only interact during erythropoiesis, defining a self-interacting erythroid compartment. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL16417

33 Samples

Download data: TXT

(Submitter supplied) The genome is organized via CTCF/cohesin binding sites, which partition chromosomes into 1-5Mb topologically associated domains (TADs), and further into smaller contact sub-domains within TADs (sub-TADs; 40-1000kb). Here we examined in vivo an ~80kb sub-TAD, containing the mouse α-globin gene cluster, lying within a ~1Mb TAD. We find that the sub-TAD is flanked by predominantly convergent CTCF/cohesin sites which are ubiquitously bound by CTCF but only interact during erythropoiesis, defining a self-interacting erythroid compartment. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL16417

10 Samples

Download data: BW

(Submitter supplied) ChIP-seq for CTCF and Rad21 in 3 week old mouse brain from reciprocal BxC and CxB crosses. One biological replicate of each.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

8 Samples

Download data: BAM

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

Organism:

Mus musculus

Type:

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

Platform:

GPL9250

25 Samples

Download data

(Submitter supplied) To ensure proper gene regulation within constrained nuclear space, chromosomes facilitate access to transcribed regions, while compactly packaging all other information. Recent studies revealed that chromosomes are organized into megabase-scale domains that demarcate active and inactive genetic elements, suggesting that compartmentalization is important for genome function. Here we show that very specific long-range interactions are anchored by cohesin/CTCF sites, but not cohesin-only or CTCF-only sites, to form a hierarchy of chromosomal loops. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL9250

13 Samples

Download data: TXT

(Submitter supplied) To ensure proper gene regulation within constrained nuclear space, chromosomes facilitate access to transcribed regions, while compactly packaging all other information. Recent studies revealed that chromosomes are organized into megabase-scale domains that demarcate active and inactive genetic elements, suggesting that compartmentalization is important for genome function. Here we show that very specific long-range interactions are anchored by cohesin/CTCF sites, but not cohesin-only or CTCF-only sites, to form a hierarchy of chromosomal loops. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

8 Samples

Download data: FPKM_TRACKING

(Submitter supplied) To ensure proper gene regulation within constrained nuclear space, chromosomes facilitate access to transcribed regions, while compactly packaging all other information. Recent studies revealed that chromosomes are organized into megabase-scale domains that demarcate active and inactive genetic elements, suggesting that compartmentalization is important for genome function. Here we show that very specific long-range interactions are anchored by cohesin/CTCF sites, but not cohesin-only or CTCF-only sites, to form a hierarchy of chromosomal loops. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

4 Samples

Download data: NARROWPEAK

(Submitter supplied) Chromosome conformation capture approaches have shown that interphase chromatin is organized into an architectural framework of Mb-sized compartments and sub-Mb-sized topological domains. Cohesin controls chromosome topology to facilitate DNA repair and chromosome segregation in cycling cells, and also associates with active enhancers and promoters and with CTCF to form long-range interactions important for gene regulation. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL9250

13 Samples

Download data: BED, TAR, TXT

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL21103 GPL17021

43 Samples

Download data

(Submitter supplied) Sequencing files provided here include 4C-seq experiments for a total of 6 viewpoints neighboring 5 highly sex-biased genes in mouse liver. These files are part of a larger study ("CTCF and Cohesin link sex-biased distal regulatory elements to sex-biased gene expression in mouse liver"), where we compare CTCF and cohesin binding in male and female mouse liver as well as differences in chromatin conformation (DNA looping).

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

36 Samples

Download data: BW

(Submitter supplied) Sequencing files provided here include mouse liver ChIP-seq for CTCF and the cohesin subunit Rad21. These files are part of a larger study ("CTCF and Cohesin link sex-biased distal regulatory elements to sex-biased gene expression in mouse liver") where we compare CTCF and cohesin binding in male and female mouse liver as well as differences in chromatin conformation (DNA looping).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

7 Samples

Download data: BED

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below, and presents the high throuput sequencing datasets that were generated as part of a larger study that investigates the role of CTCF and cohesin as key drivers of 3D-nuclear organization, anchoring the megabase-scale Topologically Associating Domains (TADs) that segment the genome. This study presents and validates a computational method to predict cohesin-and-CTCF binding sites that form intra-TAD DNA loops. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL21103 GPL17021 GPL13112

15 Samples

Download data

(Submitter supplied) Sequencing files provided here include mouse liver ChIP-seq for CTCF and the cohesin subunit Rad21. These files are part of a larger study where we describe features of Topologically Associating Domains (TADs) and their impact on liver gene expression, then use these features to computationally predict subTAD structures not otherwise readily identifiable due to the low resolution of Hi-C. Our findings reveal that CTCF-based subTAD loops maintain key insulating properties of TADs, and support the proposal that subTADs are formed by the same loop extrusion mechanism and contribute to nuclear architecture as intra-TAD scaffolds that further constrain enhancer-promoter interactions. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21103 GPL13112

7 Samples

Download data: BED

(Submitter supplied) CTCF and the cohesin complex modify chromatin by binding to DNA and interacting with each other and with other cellular proteins. Both proteins regulate transcription by a variety of local effects on transcription and by long range topological effects. CTCF and cohesin also bind to herpesvirus genomes at specific sites and regulate viral transcription during latent and lytic cycles of replication. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

9 Samples

Download data: TXT

(Submitter supplied) CTCF and the cohesin complex modify chromatin by binding to DNA and interacting with each other and with other cellular proteins. Both proteins regulate transcription by a variety of local effects on transcription and by long range topological effects. CTCF and cohesin also bind to herpesvirus genomes at specific sites and regulate viral transcription during latent and lytic cycles of replication. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

9 Samples

Download data: BW

(Submitter supplied) The DNA-binding protein CTCF and the cohesin complex function together to shape chromatin architecture in mammalian cells, but the molecular details of this process remain unclear. We demonstrate that a 79 amino acid region within the CTCF N-terminal domain but not the C-terminus is necessary for cohesin positioning at CTCF binding sites and chromatin loop formation. However, the N-terminus of CTCF, when fused to artificial zinc fingers that do not bind to CTCF DNA binding sites was not sufficient to redirect cohesin to different genomic locations, indicating that cohesin positioning by CTCF does not involve direct protein-protein interactions with cohesin subunits. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL11154 GPL13112

152 Samples

Download data: BEDGRAPH, TXT, XLSX