GEO DataSets

(Submitter supplied) Cohesin is crucial for proper chromosome segregation, but also regulates gene transcription and organism development by poorly understood mechanisms. We find that in Drosophila, cohesin functionally interacts with Polycomb group (PcG) silencing proteins at both silenced and active genes. Cohesin unexpectedly facilitates binding of Polycomb Repressive Complex 1 (PRC1) to many active genes. In contrast, cohesin and PRC1 binding are mutually antagonistic at silenced genes. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6629

19 Samples

Download data: BAR, BED, CEL

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

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL1322 GPL6629

28 Samples

Download data: BAR, BED, CEL

(Submitter supplied) Cohesin is crucial for proper chromosome segregation, but also regulates gene transcription and organism development by poorly understood mechanisms. We find that in Drosophila, cohesin functionally interacts with Polycomb group (PcG) silencing proteins at both silenced and active genes. Cohesin unexpectedly facilitates binding of Polycomb Repressive Complex 1 (PRC1) to many active genes. In contrast, cohesin and PRC1 binding are mutually antagonistic at silenced genes. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

9 Samples

Download data: CEL

(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) Depletion of architectural factors globally alters chromatin structure, but only modestly affects gene expression. We revisit the structure-function relationship using the inactive X chromosome (Xi) as a model. We investigate cohesin imbalances by forcing its depletion or retention using degron-tagged RAD21 (cohesin subunit) or WAPL (cohesin release factor). Interestingly, cohesin loss disrupts Xi superstructure, unveiling superloops between escapee genes, with minimal effect on gene repression. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL17021 GPL21103 GPL24247

94 Samples

Download data: BW, HIC, TXT

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

Organism:

Drosophila melanogaster

Type:

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

Platform:

GPL19528

86 Samples

Download data

(Submitter supplied) RNA expression was measured using RNA-seq

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19528

14 Samples

Download data: TXT

(Submitter supplied) RNA nascent transcription was measured using NT-seq

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19528

10 Samples

Download data: SGR, TXT

(Submitter supplied) Binding of RNA Polymerase, Spt5, and PRC1 subunits to chromosomes was measured by ChIP-seq

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19528

62 Samples

Download data

(Submitter supplied) Genome-wide binding profile of PcG proteins- Ph, H3K27me3 and Cg in Drosophila third instar larval brains and disks, in duplicate, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17275

8 Samples

Download data: TDF

(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:

GPL17275

35 Samples

Download data: TDF

(Submitter supplied) Genome-wide binding profile of PcG proteins Pho and Ph, H3K27me3 and Engrailed in Drosophila third instar larval brains and disks, in duplicate, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17275

11 Samples

Download data: TDF

(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) Monoubiquitinated histone H2A produced by the Sce/Ring subunit of the Polycomb Repressive Complex 1 (PRC1) was mapped genome-wide in Drosophila ML-DmBG3 cells using chromatin immunoprecipitation followed by hybridization to Affymetrix tiling arrays.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6629

1 Sample

Download data: BAR, BED, CEL

(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:

GPL6629 GPL13304

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) Polycomb Repressive Complexes 1 and 2 (PRC1, PRC2) are conserved epigenetic regulators that promote transcriptional silencing. PRC1 and PRC2 converge on shared targets, catalyzing repressive histone modifications. In addition, a subset of PRC1/PRC2 targets engage in long-range interactions whose functions in gene silencing are poorly understood. Using a CRISPR screen in mouse embryonic stem cells, we discovered that the cohesin regulator PDS5A links transcriptional silencing by Polycomb and 3D genome organization. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL21103

115 Samples

Download data: BW, CSV, HIC, MCOOL

(Submitter supplied) Polycomb group (PcG) proteins maintain the silenced state of key developmental genes in animals, but how these proteins are recruited to specific regions of the genome is still poorly understood. In Drosophila, PcG proteins are recruited to Polycomb response elements (PREs) that include combinations of sites for sequence specific DNA binding “PcG recruiters,” including Pho, Cg, and Spps. To understand their roles in PcG recruitment, we compared Pho-, Cg-, and Spps-binding sites against H3K27me3 and key PcG proteins by ChIP-seq in wild-type and mutant third instar larvae. more...

Organism:

Drosophila melanogaster

Type:

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

Platform:

GPL17275

52 Samples

Download data: TDF, TXT

(Submitter supplied) Effects of Nipped-B and Rad21 sister chromatid cohesin proteins on gene expression data in ML-DmBG3 cells derived from Drosophila melanogaster larval central nervous system We examined the effects of Nipped-B and Rad21 knockdown on gene expression in BG3 cells using microarrays that measure over 18,700 transcripts to (a) determine if the effects of cohesion on E(spl)-C and invected-engrailed expression are unique, (b) look for effects of cohesin on regulators of E(spl)-C and engrailed, and (c) obtain a comprehensive view of the effects of cohesin on gene expression.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

12 Samples

Download data: CEL, TXT