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Series GSE44566 Query DataSets for GSE44566
Status Public on Aug 10, 2013
Title Genome-wide analysis identifies a functional association of Tet1 and Polycomb PRC2 in mouse embryonic stem cells but not in differentiated tissues
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Recent studies have analyzed the distribution and role of 5-hydroxymethylcytosin (5hmC) in Embryonic Stem Cells (ESC). However, DNA hydroxymethylation occurs also in differentiated cells and it is significantly deregulated in cancer. Here we mapped 5hmC genome-wide profile in pluripotent ES cells in comparison to embryonic and adult differentiated cells. Comparative analysis of 5hmC genomic distribution with respect to gene expression reveals that 5hmC is enriched on the gene body of genes expressed at medium/high level and on TSS of genes not expressed or expressed at low level independently from the cell type. ESC showed a significant enrichment of DNA hydroxymethylation in active enhancers and bivalent promoters with respect to more differentiated cells as well as preferential association of Tet1 and 5hmC with promoter bound by Polycomb Repressive Complex 2 (PRC2). Furthermore, we show that in ESC PRC2 interacts with Tet1 and it is required for Tet1 recruitment to the chromatin and 5hmC deposition at developmental genes.
 
Overall design Examination of 5hmC in ESC, MEF, Brain, Liver, shGFP ESC, and shSuz12ESC, and examination of expression in shGFP ESC and shSuz12ESC.
Web link http://epigenetics.hugef-research.org/data.php
 
Contributor(s) Neri F, Oliviero S
Citation(s) 23987249
Submission date Feb 22, 2013
Last update date Dec 09, 2016
Contact name Francesco Neri
E-mail francesco.neri@hugef-torino.org
Organization name HuGeF
Street address Via Nizza 52
City Torino
State/province Italy
ZIP/Postal code 10126
Country Italy
 
Platforms (1)
GPL16173 Illumina HiScanSQ (Mus musculus)
Samples (8)
GSM1087009 5hmC_ESC
GSM1087010 5hmC_MEF
GSM1087011 5hmC_Brain
Relations
BioProject PRJNA190080
SRA SRP018807

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE44566_RAW.tar 249.2 Mb (http)(custom) TAR (of BED, BEDGRAPH)
Raw data are available in SRA
Processed data provided as supplementary file

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