GEO DataSets

(Submitter supplied) TF binding clusters in promoter correlate well with gene expression. We used ChIP-seq to map binding sites of the majority of highly expressed TFs in the cell. The size of clusters of TFs in the promoters of genes were found to correlate well with gene expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17394

8 Samples

Download data: CEL

(Submitter supplied) During cell division, transcription factors (TFs) are removed from chromatin twice, during DNA synthesis, and during condensation of chromosomes. How TFs can efficiently find their sites following these stages has been unclear. Here, we have analyzed the binding pattern of expressed TFs in human colorectal cancer cells. We find that binding of TFs is highly clustered, and that the clusters are enriched in binding motifs for several major TF classes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

16 Samples

Download data: TXT

(Submitter supplied) During cell division, transcription factors (TFs) are removed from chromatin twice, during DNA synthesis, and during condensation of chromosomes. How TFs can efficiently find their sites following these stages has been unclear. Here, we have analyzed the binding pattern of expressed TFs in human colorectal cancer cells. We find that binding of TFs is highly clustered, and that the clusters are enriched in binding motifs for several major TF classes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

28 Samples

Download data: TXT

(Submitter supplied) During cell division, transcription factors (TFs) are removed from chromatin twice, during DNA synthesis, and during condensation of chromosomes. How TFs can efficiently find their sites following these stages has been unclear. Here, we have analyzed the binding pattern of expressed TFs in human colorectal cancer cells. We find that binding of TFs is highly clustered, and that the clusters are enriched in binding motifs for several major TF classes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

268 Samples

Download data: TXT

(Submitter supplied) During cell division, transcription factors (TFs) are removed from chromatin twice, during DNA synthesis, and during condensation of chromosomes. How TFs can efficiently find their sites following these stages has been unclear. Here, we have analyzed the binding pattern of expressed TFs in human colorectal cancer cells. We find that binding of TFs is highly clustered, and that the clusters are enriched in binding motifs for several major TF classes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL10999 GPL11154

225 Samples

Download data: TXT

(Submitter supplied) The cohesin complex plays essential roles in sister chromatin cohesin, chromosome organization and gene expression. The role it plays in the regulation of genes is incompletely understood. Here, we report that the cohesin release factor WAPL in mouse embryonic stem cells is crucial for maintaining a pool of dynamically bound cohesin to regions in the genome that are associated with lineage specific genes. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL21626 GPL17021 GPL21273

128 Samples

Download data: BED, BW, 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:

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) Cohesin subunits, the Nipped-B cohesin loader, the MED1 and MED30 subunits of the Mediator complex, and the Fs(1)h BET domain protein were mapped by ChIP-seq in ML-DmBG3-c2 cells and their effects on each other's association with promoters, enhancers, Polycomb Response Elements, and DNA replication origins were measured. DNA replication in early S phase was measured by ChIP-seq and correlated with functional element occupancy by cohesin.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19528

58 Samples

Download data: SGR

(Submitter supplied) The cohesin complex links DNA molecules and plays key roles in the organization, expression, repair, and segregation of eukaryotic genomes. In vertebrates the Esco1 and Esco2 acetyltransferases both modify cohesin’s Smc3 subunit to establish sister chromatid cohesion during S phase, but differ in their N-terminal domains and expression during development and across the cell cycle. Here we show that Esco1 and Esco2 also differ dramatically in their interaction with chromatin, as Esco1 is recruited by cohesin to over 11,000 sites, whereas Esco2 is infrequently enriched at REST/NRSF target genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

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

Organism:

Drosophila melanogaster

Type:

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

Platform:

GPL19528

91 Samples

Download data

(Submitter supplied) RNA expression was measured by RNA-seq in Drosophila ML-DmBG3-c2 cells depleted for proteins involved in sister chromatid cohesion, and in developing third instar wing discs with or withough brca2 gene mutations

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19528

36 Samples

Download data: XLSX

(Submitter supplied) The Pds5, Wapl and Brca2 proteins were mapped by ChIP-seq, and the effects of their depletion on the binding of cohesin subunits and the Nipped-B cohesin loader were examined by ChIP-seq

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19528

55 Samples

Download data

(Submitter supplied) We employ ChIP-seq methodology to study genome-wide distribution of MCM2, NIPBL and cohesin in thymidine-arrested cells

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

7 Samples

Download data: BED, BIGWIG, BROADPEAK

(Submitter supplied) Cohesin complex, a main organizer of mammalian genomes, exists in two versions that differ in the identity of the STAG/SA subunit, which can be SA1 or SA2. Mouse embryonic stem cell (mESC) provide a useful system to address the specific contributions of each variant to genome architecture and gene expression, since 3D organization of super- enhancers and Polycomb domains is essential to achieve transcription of pluripotency factors and repression of lineage specification genes, respectively. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL19057 GPL17021

48 Samples

Download data: BW

(Submitter supplied) Mammalian genomes are organized into compartments, topologically-associating domains (TADs) and loops to facilitate gene regulation and other chromosomal functions. Compartments are formed by nucleosomal interactions, but how TADs and loops are generated is unknown. It has been proposed that cohesin forms these structures by extruding loops until it encounters CTCF, but direct evidence for this hypothesis is missing. more...

Organism:

Homo sapiens

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

30 Samples

Download data: HIC, WIG

(Submitter supplied) The main objective of this study is to determine how cohesin influences transcription and compare these changes to changes previously observed in chromatin structure, which were previously determined by Mnase-seq

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

5 Samples

Download data: BIGWIG

(Submitter supplied) The main objective of this study is to determine how cohesin influences chromatin structure and chromatin assembly during DNA replication

Organism:

Saccharomyces cerevisiae

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16028

8 Samples

Download data: WIG

(Submitter supplied) The main objective of this study is to determine how chromatin assembly during DNA replication influences cohesin deposition

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7250

7 Samples

Download data: BAR, CEL

(Submitter supplied) To understand how chromatin domains coordinate gene expression, we dissected select genetic elements organizing topology and transcription around the Prdm14 super enhancer in mouse embryonic stem cells. Taking advantage of allelic polymorphisms, we developed methods to sensitively analyze changes in chromatin topology, gene expression, and protein recruitment. We show that enhancer insulation does not strictly rely on loop formation between its flanking boundaries, that the enhancer activates the Slco5a1 gene beyond its prominent domain boundary, and that it recruits cohesin for loop extrusion. more...

Organism:

Mus musculus

Type:

Other

Platforms:

GPL28599 GPL23969 GPL19057

27 Samples

Download data: HDF5, HIC, WIG