Genome-wide analysis of histone modification, protein-DNA binding, cytosine methylation and transcriptome data in mouse and human ES cells and pig iPS cells
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ABSTRACT:
ORGANISM(S): Mus musculus Sus scrofa Homo sapiens
PROVIDER: GSE36114 | GEO | 2012/02/28
SECONDARY ACCESSION(S): PRJNA152995
REPOSITORIES: GEO
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Project description:Genome-wide analysis of histone modification (H2AZ, H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me2, H3K4me3 and H3K9me3), protein-DNA binding (TAF1, P300, Pou5f1 and Nanog), cytosine methylation and transcriptome data in mouse and human ES cells and pig iPS cells We generated histone modification data (H2AZ, H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me2, H3K4me3 and H3K9me3) and protein-DNA binding data (TAF1, P300, Pou5f1 and Nanog) using Chromatin Immunoprecipitation followed by short sequencing (ChIP-seq), cytosine methylation data using methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) and DNA digestion by methyl-sensitive restriction enzymes followed by sequencing (MRE-seq), transcriptome data with RNA short sequencing (RNA-seq) in human embryonic stem cells, mouse embryonic stem cells, pig induced pluripotent stem cells and mouse embryonic stem cells under activin-A-induced-differentiation. Examination of 8 histone modifications, 4 protein-DNA binding, cytosine methylation and transcriptome in human embryonic stem cells, mouse embryonic stem cells, pig induced pluripotent stem cells and mouse embryonic stem cells under activin-A-induced-differentiation.
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Project description:Genetic control of pluripotent mammalian ES cells is determined by a transcriptional network, with a "central core" of transcription factors, Pou5f1, Sox2 and Nanog. Zebrafish homologues of the "core pluripotency factors" Pou5f1, SoxB1 and Nanog-like are also crucially involved in early development. However, the degree of functional similarity of the network between mammals and non-mammals is a matter of debate. To identify the components of Pou5f1-dependent transcriptional networks, we determined the genomic binding sites for Pou5f1 and Sox2 in late blastula stage zebrafish embryos using ChIP-seq. We found that Sox2 and Pou5f1 are co-binding to the regulatory regions of Sox2, Pou5f1, and Nanog-like, as well as to multiple orthologues of mammalian plutipotency network components. Deep sequencing was performed using the Illumina GAIIx on DNA samples obtained from Sox2 ChIP, Pou5f1-Flag ChIP and Input Control. Pou5f1 was analysed in technical duplicates to obtain higher sequencing depth.
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