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Series GSE31343 Query DataSets for GSE31343
Status Public on Nov 24, 2011
Title 5-hydroxymethylcytosine: the sixth DNA base
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary We performed a meta analysis of publicly available TET1, 5mC, 5hmC and genome wide bisulfite profiling data mostly from mouse embryonic stem cells (ESC). Genome wide chromatin immunoprecipitation combined with deep sequencing (ChIP-seq) has revealed binding of the TET1 protein at CpG-island (CGI) promoters and at bivalent promoters. We show that TET1 also coincides with DNAseI hypersensitive sites (HS). Presence of TET1 at these THREE locations suggests that it may play a dual role: an active role at CpG-islands and DNAseI hypersensitive sites and a repressive role at bivalent loci. In line with the presence of TET1, significant enrichment of 5hmC but not 5mC is detected at bivalent promoters and DNaseI HS. Surprisingly, 5hmC is not detected or present at very low levels at CGI promoters notwithstanding the presence of TET1 at these loci. Our meta analysis suggest that asymmetric methylation is present at CA- and CT-repeats in the genome of some human ESC.
Overall design Examination of the distribution of 5-methylcytosine and 5-hydroxymethylcytosine in the genome of mouse embryonic stem cells.
Contributor(s) Stunnenberg HG, Carrillo-de Santa Pau E, Matarese F
Citation(s) 22186736
Submission date Aug 11, 2011
Last update date May 15, 2019
Contact name H.G. Stunnenberg
Phone +31-24-3610520
Organization name Radboud University
Department Department of Molecular Biology (274)
Street address Geert Grooteplein 28
City Nijmegen
ZIP/Postal code 6525 GA
Country USA
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (5)
GSM777313 MethylCap-seq_medium
GSM777314 MethylCap-seq_high
SRA SRP007839
BioProject PRJNA145929

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Supplementary file Size Download File type/resource
GSE31343_RAW.tar 424.3 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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