GEO DataSets

(Submitter supplied) Histone variant H2A.Z occupies the promoters of active and poised, bivalent genes in ESCs to regulate developmental programs, yet how it contributes to these contrasting states is poorly understood. Here, we investigate the function of H2A.Z.1 mono-ubiquitylation (H2A.Z.1ub) by mutation of the PRC1 target residues (H2A.Z.1K3R3). We show that H2A.Z.1K3R3 is properly incorporated at target promoters in murine ESCs (mESCs), however, loss of mono-ubiquitylation leads to de-repression of bivalent genes, loss of Polycomb binding, and to faulty lineage commitment. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

3 Samples

Download data: TXT

(Submitter supplied) Histone variant H2A.Z occupies the promoters of active and poised, bivalent genes in ESCs to regulate developmental programs, yet how it contributes to these contrasting states is poorly understood. Here, we investigate the function of H2A.Z.1 mono-ubiquitylation (H2A.Z.1ub) by mutation of the PRC1 target residues (H2A.Z.1K3R3). We show that H2A.Z.1K3R3 is properly incorporated at target promoters in murine ESCs (mESCs), however, loss of mono-ubiquitylation leads to de-repression of bivalent genes, loss of Polycomb binding, and to faulty lineage commitment. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

10 Samples

Download data: BED, WIG

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL11002 GPL13112

5 Samples

Download data: BED, WIG

(Submitter supplied) Histone variant H2A.Z occupies the promoters of active and poised, bivalent genes in ESCs to regulate developmental programs, yet how it contributes to these contrasting states is poorly understood. Here, we investigate the function of H2A.Z.1 mono-ubiquitylation (H2A.Z.1ub) by mutation of the PRC1 target residues (H2A.Z.1K3R3). We show that H2A.Z.1K3R3 is properly incorporated at target promoters in murine ESCs (mESCs), however, loss of mono-ubiquitylation leads to de-repression of bivalent genes, loss of Polycomb binding, and to faulty lineage commitment. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

2 Samples

Download data: BED, WIG

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL11002

9 Samples

Download data: BED, BIGWIG

(Submitter supplied) The H2A variant H2AZ is essential for embryonic development and for proper execution of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions in H2AZ are likely key for its functional specialization, but we know little about how these differences contribute to chromatin regulation. Here, we show that the extended acidic patch, specifically the three divergent residues in the C-terminal docking domain, is necessary for lineage commitment during ESC differentiation and proper execution of gene expression programs during ESC differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT

(Submitter supplied) The H2A variant H2AZ is essential for embryonic development and for proper execution of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions in H2AZ are likely key for its functional specialization, but we know little about how these differences contribute to chromatin regulation. Here, we show that the extended acidic patch, specifically the three divergent residues in the C-terminal docking domain, is necessary for lineage commitment during ESC differentiation and proper execution of gene expression programs during ESC differentiation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

3 Samples

Download data: BED, BIGWIG

(Submitter supplied) Chromatin modifications have been implicated in the self-renewal and differentiation of embryonic stem cells (ESCs). However, the function of histone variant H2A.Z in ESCs remains unclear. We show that H2A.Z is highly enriched at promoters and enhancers and is required for both efficient self-renewal and differentiation of murine ESCs. H2A.Z deposition leads to an abnormal nucleosome structure, decreased nucleosome occupancy and increased chromatin accessibility. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL11002

42 Samples

Download data: BED

(Submitter supplied) The transcriptional repressors Polycomb Repressive Complex 1 (PRC1) and PRC2 are required to maintain cell fate during embryonic development. PRC1 and PRC2 catalyse distinct histone modifications, establishing repressive chromatin at shared targets. Loss of PRC1, but not PRC2, from mouse embryonic stem cells (mESCs) triggers exit from pluripotency. How PRC2 and PRC1, which consists of distinct “variant PRC1” (vPRC1) and “canonical PRC1” (cPRC1) complexes, cooperate to silence genes and support mESC self-renewal is unclear. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

198 Samples

Download data: BW, TSV

(Submitter supplied) The goal of this study is to compare total RNA expression profiles among wild type, MMTR knock down, and overexpression of full length, C-terminal and N-terminal in G-CCE cells at d0 and d3 after differentiation. All cell lines were maintained in DMEM supplemented with 15% heat-inactivated fetal bovine serum (FBS; Gibco, 16141079), 1X MEM Non-Essential Amino Acids Solution (Sigma-Aldrich, M7145), 300 μM monothioglycerol (Sigma-Aldrich, M6145), 1X penicillin/streptomycin, and 1000 U/ml Leukima inhibitory factor (LIF, Sigma-Aldrich, ESG1107) in 0.1% gelatin coated cell culture dishes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

10 Samples

Download data: TXT

(Submitter supplied) The essential histone variant H2A.Z localises to both active and silent chromatin sites. In embryonic stem cells (ESCs), H2A.Z is also reported to co-localise with polycomb repressive complex 2 (PRC2) at developmentally silenced genes. The mechanism of H2A.Z targeting is not clear, but a role for the PRC2 component Suz12 has been suggested. Given this association, we wished to determine if polycomb functionally directs H2A.Z incorporation in ESCs. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL14936

10 Samples

Download data: PAIR, TXT

(Submitter supplied) The histone variant H2A.Z has been implicated in nucleosome exchange, transcriptional activation and Polycomb repression. However, the relationships among these seemingly disparate functions remain obscure. We mapped H2A.Z genome-wide in mammalian ES cells and neural progenitors. H2A.Z is deposited promiscuously at promoters and enhancers, and correlates strongly with H3K4 methylation. Accordingly, H2A.Z is present at poised promoters with bivalent chromatin and at active promoters with H3K4 methylation, but is absent from stably repressed promoters that are specifically enriched for H3K27 trimethylation. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9052 GPL9185

7 Samples

Download data: BW

(Submitter supplied) Two distinct Polycomb complexes, PRC1 and PRC2, collaborate to maintain epigenetic repression of key developmental loci in embryonic stem cells (ESCs). PRC1 and PRC2 have histone modifying activities, catalyzing mono-ubiquitination of histone H2A (H2AK119u1) and trimethylation of H3 lysine 27 (H3K27me3) respectively. Compared to H3K27me3, localization and role of H2AK119ub1 is not fully understood in ESCs. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL14573 GPL1261 GPL14597

40 Samples

Download data: CEL, TXT

(Submitter supplied) ChIP-on-chip analysis was carried out to determine targets of Ring1B, Ring1A, H2AK119u1 and H3K27me3 in mouse ES cells.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by array

Platforms:

GPL14597 GPL14573

28 Samples

Download data: TXT

(Submitter supplied) We used microarrays to investigate the restoration of repression of PRC1 target gene expression in Ring1A/B-dKO ES cells stably expressing either of mock, WT or mutant Ring1B construct.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

12 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

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

Platform:

GPL24247

43 Samples

Download data: BED, BIGWIG, BW, GTF, NARROWPEAK

(Submitter supplied) This study describes the transcriptome profiling of day 6 SFEBq embryonic bodies (EBs): 1) WT; 2) Wdr5 KO ; 3) Wdr5 KO with T12h hWDR5 rescue; 4) Wdr5 KO with T48h hWDR5 rescue

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

18 Samples

Download data: GTF

(Submitter supplied) This study describes the binding profile of MAX in mouse embryonic bodies at day 2 (WT, Wdr5 KO, Wdr5 and p53 double knockout)

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

3 Samples

Download data: NARROWPEAK

(Submitter supplied) This study describes the binding profile of WDR5 and H3K4me3 in Wdr5 and p53 double knockout ESC rescued with WDR5WT or WDR5S91KY191F

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) This study describes time-course chromatin accessibility profiling of mouse ESC and embryonic bodies n Wdr5 and p53 knockout (with or without WT or mutant hWDR5 rescue)

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

16 Samples

Download data: BED, BW, NARROWPEAK