Transcriptomics

Dataset Information

63

Expression data from Chd1-deficient mouse ES cells (E14 cell lines) and genome-wide binding of Chd1 in parental ES cells


ABSTRACT: We used microarrays to study the effect of Chd1 loss of function in mouse ES cells. We used ChIP-chip to analyze genome-wide binding of Chd1 in normal ES cells. Mouse Embryonic Stem (ES) cells were infected with a lentiviral vector (pSicoR-mCherry) for expression of a shRNA against Chd1 and GFP (as a control). mCherry-sorted ES cells were plated and individual clones were selected and grown under normal ES cell conditions. 6 ES cell clonal lines were isolated and analyzed along with the parental E14 cell line. The final analysis consisted in 3 control cell lines (E14, E1 and G8) and 4 Chd1-deficient cells (3 different clones using a shRNA sequence #1- C1i5, C1i6 and C1i9; 1 clone using a different shRNA (#4) sequence targeting Chd1- C4i2). RNA samples were isolated from these Chd1-deficient ES cells and control ES cells, and hybridized on Affymetrix chip. For ChIP-chip, parental E14 ES cell line was used.

ORGANISM(S): Mus musculus  

SUBMITTER: Michael T McManus   Amy Heidersbach  Kathrin Plath  Miguel Ramalho-Santos  Fanny Polesso  Eran Meshorer  Adi Alajem  Alexandre Gaspar-Maia  Rupa Sridharan  João Ramalho-Santos  Michael Mason 

PROVIDER: E-GEOD-16462 | ArrayExpress | 2009-08-13

SECONDARY ACCESSION(S): GSE16462PRJNA116039

REPOSITORIES: GEO, ArrayExpress

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Publications


An open chromatin largely devoid of heterochromatin is a hallmark of stem cells. It remains unknown whether an open chromatin is necessary for the differentiation potential of stem cells, and which molecules are needed to maintain open chromatin. Here we show that the chromatin remodelling factor Chd1 is required to maintain the open chromatin of pluripotent mouse embryonic stem cells. Chd1 is a euchromatin protein that associates with the promoters of active genes, and downregulation of Chd1 le  ...[more]

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