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Polycomb-dependent H3K27me1 and H3K27me2 regulate active transcription and enhancer fidelity

ABSTRACT: These data include the genome wide location of different histone modifications by ChIP sequencing in mouse ES cells, and RNA Seq data generated from wild type and EED KO mouse ES cells and knocked down for unrelated protein and Setd2 protein.

ORGANISM(S): Mus musculus

PROVIDER: GSE51006 | GEO | 2013/12/05

SECONDARY ACCESSION(S): PRJNA219508

REPOSITORIES: GEO

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Polycomb-dependent H3K27me1 and H3K27me2 regulate active transcription and enhancer fidelity

Project description:These data include the genome wide location of different histone modifications by ChIP sequencing in mouse ES cells, and RNA Seq data generated from wild type and EED KO mouse ES cells and knocked down for unrelated protein and Setd2 protein. ChIP-Seq: Immuno-precipitation of formaldehyde cross-linked chromatin prepared from wild type mouse E14 ES cells, wild type E36 ES cells, EED KO E36 ES cells, wild type Embryoid bodies (Ebs), EED KO Embryoid bodies (Ebs EED KO) using specific antibody against different histone modifications. RNA-Seq: Total RNA extracted from wild type E36 ES cells, EED KO E36 ES cells, wild type E36 Embryoid bodies (Ebs), EED KO Embryoid bodies (Ebs EED KO), E14 Ctrl KD, E14 Setd2 KD.

2013-12-05 | E-GEOD-51006 | biostudies-arrayexpress

Polycomb-dependent H3K27me1 and H3K27me2 characterization in mouse ES cells (E36 with H3K27ac, H3K27me1, and H3K4me1/3)

Project description:These data include the genome wide location analysis of H3K27me1/2/ac and H3K4me1/3 by ChIP in mouse ES cells.

2013-12-05 | GSE39496 | GEO

Polycomb-dependent H3K27me1 and H3K27me2 characterization in mouse ES cells (E14 and E36 with H3K27me1/2 and H3)

Project description:These data include the genome wide location analysis of H3K27me1/2/ac and H3K4me1/3 by ChIP in mouse ES cells.

2013-12-11 | GSE40109 | GEO

Polycomb-dependent H3K27me1 and H3K27me2 characterization in mouse ES cells (E36 with H3K27ac, H3K27me1, and H3K4me1/3)

Project description:These data include the genome wide location analysis of H3K27me1/2/ac and H3K4me1/3 by ChIP in mouse ES cells. Precipitation of formaldehyde cross-linked chromatin prepared from mouse ES cell using specific antibodies against Histone H3 and its specific modifications. Rabbit IgG were used as control.

2013-12-05 | E-GEOD-39496 | biostudies-arrayexpress

Polycomb-dependent H3K27me1 and H3K27me2 characterization in mouse ES cells (E14 and E36 with H3K27me1/2 and H3)

2013-12-11 | E-GEOD-40109 | biostudies-arrayexpress

Polycomb-dependent H3K27me1 and H3K27me2 characterization in mouse ES cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-12-05 | GSE40118 | GEO

Polycomb-dependent H3K27me1 and H3K27me2 characterization in mouse ES cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-12-05 | E-GEOD-40118 | biostudies-arrayexpress

Expression regulation by RYBP in mouse embryonic stem cells

Project description:Polycomb repressive complexes (PRCs) are important chromatin regulators of ES cell function. RYBP binds Polycomb H2A monoubiquitin ligases Ring1A and Ring1B, and has been suggested to participate in localizing Polycomb complexes to their targets. Moreover, constitutive inactivation of RYBP precludes ES cell formation. Here we have used ES cells conditionally deficient in RYBP to investigate RYBP function. Chromosome immunoprecipitation on a chip (ChIP-chip) of RYBP and microarray experiments were performed using wild type and knocked-out ES cells. Gene expression profiling of WT, conditionally deficient in RYBP with or without Yaf2 RNAi, and ChIP-chip of RYBP on promoters of WT, Dnmt1-KO or Eed-KO ES cells.

2012-04-03 | E-GEOD-32294 | biostudies-arrayexpress

Transcription profiling of mouse ES cells and various differentiated cell types

Project description:We used microarrays to detail the role of Polycomb proteins including Ezh2 and Eed in maintaining ES cell identity and executing pluripotency. Experiment Overall Design: To assay the global effects of the loss of polycomb proteins (Ezh2 or Eed) in embryonic stem (ES) cells , we compared the expression profiles of homologuous Ezh2 or Eed knockout ES cells to wild-type ES cells in undifferentiated or differentiated condition.

2009-01-14 | E-GEOD-12982 | biostudies-arrayexpress

PRC2 molecule EED is a target of epigenetic therapy of neuroblastoma

Project description:Epigenetic modification by polycomb repressive complex (PRC) molecules appears to have a role in tumorigenesis and aggressiveness of neuroblastoma (NB). Embryonic Ectoderm Development (EED) is a member of PRC2 complex and binds the H3K27me3 mark deposited by EZH2, via propagation on adjacent nucleosomes. Here we studied the molecular roles of EED in MYCN-amplified neuroblastoma cells by using EED-knocked down shRNAs, EED-knocked out sgRNAs, and EED small molecule inhibitor EED226. EED suppression profoundly inhibited the NB cell proliferation and flat-and soft agar colony formation. Transcriptome analysis by microarray of the EED-KD NB cells indicated the de-repression of the cell cycle regulated and differentiation-related genes; GSEA analysis results suggested that cell cycle repressed gene sets were strongly upregulated. Further, epigenetic treatment by the combination of EED inhibitor EED226 and HDAC inhibitor valproic acid effectively suppressed NB cell proliferation and colony formation. The combinatory epigenetic treatment up-regulated the cell cycle regulation- and differentiation-related genes.

2022-09-03 | GSE183369 | GEO

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