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Series GSE47793 Query DataSets for GSE47793
Status Public on Apr 28, 2014
Title The DNA methylome of Epiblast Stem Cells and Embryonic Stem Cells is distinct and not fully reversible
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Embryonic Stem Cells (ESCs) and Epiblast Stem Cells (EpiSCs) are the in vitro representants of naïve and primed pluripotency, respectively. It is currently unclear how their epigenome underpin the phenotypic and molecular characteristics of these states of pluripotency. Here, we performed the first qualitative and quantitative comparison of DNA methylation between ESCs and EpiSCs. The global level and genomic distribution of DNA methylation were very similar between the two cell types. However, the analysis of promoter methylation patterns in EpiSCs revealed several distinct features: (i) the repression of germline-related genes by DNA methylation, a process already ongoing in ESCs but far more pronounced in EpiSCs; (ii) the hypermethylation of promoters (especially CpG rich) in EpiSC compared to both ESCs and dissected epiblasts from E6.5 and E7.5 embryos; (iii) the inability of hypomethylated (Dnmt-deficient) ESCs to be converted into EpiSCs despite their ability to self-renew. Altogether, our data show that DNA methylation is an important epigenetic regulator of gene expression in EpiSCs and suggest that it is essential for the obtention of EpiSCs.
Overall design MethylCap-Seq (DNA methylation profiling) and RNA-Seq of 3 EpiStem Cells (EpiSCs) and 1 Embryonic Stem Cell line of which the data has been submitted to GEO before (part of GEO SuperSeries GSE23943 and GSE31343)
Contributor(s) Marks H, Veillard A, Bernardo A, Jouneau L, Denis L, Boulanger L, Kaan A, Brochard V, Stunnenberg HG, Jouneau A
Citation(s) 24738887
Submission date Jun 10, 2013
Last update date May 15, 2019
Contact name Hendrik Marks
Organization name Radboud University Nijmegen, RIMLS
Department Molecular Biology
Street address Geert Grooteplein 26/28
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (6)
GSM1159710 EpiSC_1_FT_8.73_p15_MethylCap-Seq
GSM1159711 EpiSC_2_FT_3.83_p24_MethylCap-Seq
GSM1159712 EpiSC_3_FT_9.73_p11_MethylCap-Seq
BioProject PRJNA207817
SRA SRP024437

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Supplementary file Size Download File type/resource
GSE47793_RAW.tar 495.4 Mb (http)(custom) TAR (of BED, WIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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