Rybp ChIP-chip in mouse ES cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE32289 | GEO | 2012/04/04
SECONDARY ACCESSION(S): PRJNA154507
REPOSITORIES: GEO
Similar Datasets
Project description:Rybp binding in wild-type, Eed-KO, and Dnmt1-KO ES cells ChIP on chip analysis was carried out using the Mouse Promoter ChIP-on-chip Microarray Set (G4490A, Agilent-014716 and Agilent-014717, Palo Alto, Calif., USA). ESCs were subjected to ChIP assay using a Rybp antibody (Santa Cruz; H-115). Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification as described previously (van Bakel et al., 2008). Labeling, hybridization and washing were carried out according to the Agilent mammalian ChIP-on-chip protocol (ver.9.0). Scanned images were quantified with Agilent Feature Extraction software under standard conditions.
2012-04-03 | E-GEOD-32289 | biostudies-arrayexpress
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
Project description:Gene expression change by Yaf2 KD in wild type or RYBP KO ES cells.
2012-04-04 | GSE32288 | GEO
Project description:Gene expression change by Yaf2 KD in wild type or RYBP KO ES cells. Total RNAs were extracted from the respective ES cells, and were subjected to microarray analysis using Affymetrix GeneChip Mouse Genome 430A 2.0 arrays
2012-04-03 | E-GEOD-32288 | biostudies-arrayexpress
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. This SuperSeries is composed of the SubSeries listed below.
2012-04-04 | GSE32294 | GEO
Project description:We used microarrays to investigate a global change in gene expression by conditional depletion of Rybp in mouse ES cells. Total RNAs were extracted from wild-type and Rybp-deficient ES cells, and were subjected to microarray analysis using Affymetrix GeneChip Mouse Genome 430A 2.0 arrays
2012-04-03 | E-GEOD-32287 | biostudies-arrayexpress
Project description:We used microarrays to investigate a global change in gene expression by conditional depletion of Rybp in mouse ES cells.
2012-04-04 | GSE32287 | GEO
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
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
Project description:Ring1 and Yy1 binding protein (Rybp) has been implicated in transcriptional regulation, apoptotic signaling and as a member of the polycomb repressive complex 1, it has an important function in regulating pluripotency and differentiation of embryonic stem cells (ESCs). Earlier, we had proved that Rybp plays an essential role in mouse embryonic and central nervous system development. This work identifies Rybp, as a critical regulator of heart development. Rybp is readily detectable in the developing mouse heart from day 8.5 of embryonic development. Prominent Rybp expression persists during all embryonic stages, and Rybp marks differentiated cell types of the heart. By utilizing rybp null ESCs in an in vitro cardiac differentiation assay, we found that rybp null ESCs do not form rhythmically beating cardiomyocytes (CMCs). Gene expression profiles revealed a downregulation of cardiac terminal and upregulation of germline-specific markers in the rybp null CMCs. Furthermore, transcriptome analysis uncovered a number of novel candidate target genes regulated by Rybp. Among these are several that are important in cardiac development and contractility such as Plagl1, Isl1, and Tnnt2. Importantly, forced expression of rybp in rybp-deficient ESCs by a lentiviral vector was able to rescue the mutant phenotype. Our data provide evidence for a previously unrecognized function of Rybp in heart development and point out the importance of germ cell lineage gene silencing during somatic differentiation.
2020-05-29 | GSE151349 | GEO