GEO DataSets

(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) 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) The cohesin complex is a chromosomal component required for sister chromatid cohesion that is conserved from yeast to man. The similarly conserved Nipped-B protein is needed for cohesin to bind to chromosomes. In higher organisms, Nipped-B and cohesin regulate gene expression and development by unknown mechanisms. Using chromatin immunoprecipitation, we find that Nipped-B and cohesin bind to the same sites throughout the entire non-repetitive Drosophila genome. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6016

8 Samples

Download data: CEL, SGR, XLS

(Submitter supplied) Binding of sister chromatid cohesion and RNA-bindng proteins to chromosomes was measured by ChIP-seq

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19528

53 Samples

Download data: SGR

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

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by high throughput sequencing

Platforms:

GPL13304 GPL6629

14 Samples

Download data: BAR, BED, BEDGRAPH, CEL

(Submitter supplied) Cohesin is a well-known mediator of sister chromatid cohesion, but it also influences gene expression and development. These non-canonical roles of cohesin are not well understood, but are vital: gene expression and development are altered by modest changes in cohesin function that do not disrupt chromatid cohesion. To clarify cohesin’s roles in transcription, we measured how cohesin controls RNA polymerase II (Pol II) activity by genome-wide chromatin immunoprecipitation and precision global run-on sequencing. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

6 Samples

Download data: BEDGRAPH

(Submitter supplied) Cohesin is a well-known mediator of sister chromatid cohesion, but it also influences gene expression and development. These non-canonical roles of cohesin are not well understood, but are vital: gene expression and development are altered by modest changes in cohesin function that do not disrupt chromatid cohesion. To clarify cohesin’s roles in transcription, we measured how cohesin controls RNA polymerase II (Pol II) activity by genome-wide chromatin immunoprecipitation and precision global run-on sequencing. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6629

8 Samples

Download data: BAR, BED, CEL

(Submitter supplied) RNA expression in wild-type and Nipped-B heterozygous mutant wing discs was quantified by RNA-seq and compared

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19528

6 Samples

Download data: XLSX

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

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

28 Samples

Download data: RDS

(Submitter supplied) It is currently assumed that 3D chromosomal organisation plays a central role in transcriptional control. However, recent evidence shows that steady-state transcription of only a minority of genes is affected by depletion of architectural proteins such as cohesin and CTCF. Here, we have used Capture Hi-C to interrogate the dynamics of chromosomal contacts of all human gene promoters upon rapid architectural protein degradation. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

16 Samples

Download data: RDS

(Submitter supplied) It is currently assumed that 3D chromosomal organisation plays a central role in transcriptional control. However, recent evidence shows that steady-state transcription of only a minority of genes is affected by depletion of architectural proteins such as cohesin and CTCF. Here, we have used Capture Hi-C to interrogate the dynamics of chromosomal contacts of all human gene promoters upon rapid architectural protein degradation. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

12 Samples

Download data: TSV

(Submitter supplied) In addition to mediating sister chromatid cohesion, cohesin plays a central role in DNA looping and segmentation of the genome into contact domains (TADs). Two variant cohesin complexes that contain either STAG/SA1 or SA2 are present in all cell types. Here we addressed their specific contribution to genome architecture in non-transformed human cells. We found that cohesin-SA1 drives stacking of cohesin rings at CTCF-bound sites and thereby contributes to the stabilization and preservation of TAD boundaries. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL18573 GPL16791 GPL11154

45 Samples

Download data: BW, TXT

(Submitter supplied) To model and characterize the chromatin regulatory landscape in Neural stem cell before and after Phf2 knockout, we performed HiC to map large-scale 3D architectural rewiring in WT and Phf2-KO NSC.

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

2 Samples

Download data: HIC

(Submitter supplied) The precise regulation of neural stem cell quiescence and activation is crucial for normal brain development and lifelong neurogenesis. However, the mechanisms that control neural stem cell activation remains poorly understood. In this study, we investigate the role of Rad21 in this process.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

9 Samples

Download data: TXT

(Submitter supplied) The precise regulation of neural stem cell quiescence and activation is crucial for normal brain development and lifelong nwurogenesis. However, the mechanisms that control neural stem cell activation remains poorly understood. In this study, we investigate the role of Phf2 in this process.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: TXT

(Submitter supplied) Chromosome segregation in mitosis and meiosis depends on sister chromatid cohesion mediated by cohesin complexes. Mutation of cohesin and other cohesion proteins causes transcriptional and developmental defects in animals and humans, but the molecular cause of these phenotypes is unknown. Here we describe 8811 cohesin binding sites in the human genome and show that the CCCTC-binding factor (CTCF) is associated with 88% of these. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

17 related Platforms

50 Samples

Download data: CEL

(Submitter supplied) The key transcription factors that control the embryonic stem cell gene expression program have been identified, but how they function to implement this program is not well understood. While screening for genes essential for maintenance of ES cell state, we identified many components of the Mediator and Cohesin complexes. Mediator and Cohesin were found to physically and functionally connect the enhancers and core promoters of active genes. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

17 Samples

Download data: TXT, WIG

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL4134 GPL9250

22 Samples

Download data: TXT, WIG