Transcriptomics,Genomics

Dataset Information

121

Epigenome and transcriptome of naive pluripotent mouse embryonic stem (ES) cells cultured in 2i serum-free medium


ABSTRACT: This study describes the epigenetic and transcriptome profiling of mouse ES cells cultures in 2i serum-free medium. The proteins for which ChIP-Seq profiles were generated in these cells, as well as for cells grown in serum conditions, include H3K4me3, H3K36me3, H3K27me3, H3K9me3, Suz12 and Ezh2. A sequence profile of genomic DNA is also included. Furthermore, we included RNA-Seq of ds_cDNA synthesized from double poly(A) selected mRNA and from rRNA depleted (strand specific) total RNA. ChIP-Seq profiling and RNA-Seq profiling on mouse naive ES cells

ORGANISM(S): Mus musculus  

SUBMITTER: Helmut Hofemeister  Andrea Kranz   Roberta Menafra   Hendrik G Stunnenberg   Austin Smith   Sergey Denissov   Kenneth Jones   Jennifer Nichols   Hendrik Marks   A F Stewart   Tüzer Kalkan    

PROVIDER: E-GEOD-23943 | ArrayExpress | 2012-11-06

SECONDARY ACCESSION(S): GSE23943SRP003412PRJNA130405

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications


Mouse embryonic stem (ES) cells grown in serum exhibit greater heterogeneity in morphology and expression of pluripotency factors than ES cells cultured in defined medium with inhibitors of two kinases (Mek and GSK3), a condition known as "2i" postulated to establish a naive ground state. We show that the transcriptome and epigenome profiles of serum- and 2i-grown ES cells are distinct. 2i-treated cells exhibit lower expression of lineage-affiliated genes, reduced prevalence at promoters of the  ...[more]

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