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Series GSE27613 Query DataSets for GSE27613
Status Public on Mar 30, 2011
Title Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells
Organism Mus musculus
Experiment type Methylation profiling by genome tiling array
Summary Recent studies have demonstrated that the Ten-eleven translocation (Tet) family proteins can enzymatically convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). While 5mC has been studied extensively, little is known about the distribution and function of 5hmC. Here we present a genome-wide profile of 5hmC in mouse embryonic stem (ES) cells. A combined analysis of global 5hmC distribution and gene expression profile in wild-type and Tet1-depleted ES cells revealed suggests that 5hmC is enriched at both gene bodies of actively transcribed genes and extended promoter regions of Polycomb-repressed developmental regulators. Thus, our study reveals the first genome-wide 5hmC distribution in pluripotent stem cells and supports its dual function in regulating gene expression.
 
Overall design Genomic DNA extracted from control (Con) or Tet1 knockdown (KD) mouse ES cells was immunoprecipitated with 5-hydroxymethylcytosine (5hmC) antibodies and analyzed by NimbleGen 2.1M mouse whole genome tiling microarrays (a 4-array set covering the entired non-repetitive portion of mouse genome). Whole cell extract (WCE) was used as input controls in IP/input experiments.
 
Contributor(s) Wu H, D'Alessio A, Ito S, Wang Z, Zhao K, Sun Y, Cui K, Zhang Y
Citation(s) 21460036
Submission date Mar 01, 2011
Last update date Jun 05, 2012
Contact name Hao Wu
E-mail(s) haowu7@gmail.com
Phone 617-713-8660
Organization name Harvard Medical School/HHMI
Department Genetics
Lab Yi Zhang
Street address 149G Warren Alpert Building, 200 Longwood Avenue
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
 
Platforms (4)
GPL7523 NimbleGen mouse (mm8) whole genome tiling array 1 of 4 [2007-08-17_MM8_Economy_01]
GPL7524 NimbleGen mouse (mm8) whole genome tiling array 2 of 4 [2007-08-17_MM8_Economy_02]
GPL7525 NimbleGen mouse (mm8) whole genome tiling array 3 of 4 [2007-08-17_MM8_Economy_03]
Samples (10)
GSM684514 Con KD ES cells, 5-hydroxymethylcytosine by hMeDIP-chip, Rb Ab (1/4)
GSM684515 Con KD ES cells, 5-hydroxymethylcytosine by hMeDIP-chip, Rb Ab (2/4)
GSM684516 Con KD ES cells, 5-hydroxymethylcytosine by hMeDIP-chip, Rb Ab (3/4)
Relations
BioProject PRJNA138263

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
GSE27613_RAW.tar 1.2 Gb (http)(custom) TAR (of PAIR)
Raw data provided as supplementary file
Processed data included within Sample table

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