 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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] |
| GPL7526 |
NimbleGen mouse (mm8) whole genome tiling array 4 of 4 [2007-08-17_MM8_Economy_04] |
|
| 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) |
| GSM684517 |
Con KD ES cells, 5-hydroxymethylcytosine by hMeDIP-chip, Rb Ab (4/4) |
| GSM684518 |
Tet1 KD ES cells, 5-hydroxymethylcytosine by hMeDIP-chip, Rb Ab (1/4) |
| GSM684519 |
Tet1 KD ES cells, 5-hydroxymethylcytosine by hMeDIP-chip, Rb Ab (2/4) |
| GSM684520 |
Tet1 KD ES cells, 5-hydroxymethylcytosine by hMeDIP-chip, Rb Ab (3/4) |
| GSM684521 |
Tet1 KD ES cells, 5-hydroxymethylcytosine by hMeDIP-chip, Rb Ab (4/4) |
| GSM684522 |
Con KD ES cells, 5-hydroxymethylcytosine by hMeDIP-chip, Rat Ab (4/4) |
| GSM684523 |
Tet1 KD ES cells, 5-hydroxymethylcytosine by hMeDIP-chip, Rat Ab (4/4) |
|
| Relations |
| BioProject |
PRJNA138263 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE27613_RAW.tar |
1.2 Gb |
(http)(custom) |
TAR (of PAIR) |
| Processed data included within Sample table |
|
|
|
|
 |
Less...
More...