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| Status |
Public on Nov 17, 2012 |
| Title |
Genome-wide maps of 5hmC state in pluripotent and (T-)iPS induction cells. |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
We performed 5hmC DNA Immunoprecipitation followed high-throughput sequencing using R1 ESCs, OT ESCs, TSKM ESCs, Day3 TSKM and OSKM induction cells. We compared the profiling of 5-hydroxymethylcytosine modifications in these different cell lines. We found that: the TSKM and OT iPSCs shared similar 5hmC modification pattern while apart from that of R1 ESCs. However the comparison based on the gene promoter (-1000/+500 of gene’s TSS) showed less differences. The TSKM 2nd induction samples were quite like each other and have shared the basic pattern with traditional OSKM 2nd sample. However comparison based on the gene promoter showed sharp increase. Moreover higher enrichment of 5hmC on the distal enhancer of Oct4 was specifically detected in Day 3 TSKM 2nd cells as well as TSKM and OT iPSCs, which might be helpful for us to study the Tet1-mediated somatic reprogramming.
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| |
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| Overall design |
Examination of 5-hydroxymethylcytosine modifications in 5 different cell lines.
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| |
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| Contributor(s) |
Gao Y, Chen J, Cai T, Gao S |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Nov 17, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Tao Cai |
| E-mail(s) |
caitao@nibs.ac.cn
|
| Organization name |
National Institute Of Biological Sciences, Beijing (NIBS)
|
| Lab |
Sequencing Facility
|
| Street address |
No. 7 Science Park Road, Zhongguancun Life Science Park
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
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| Platforms (1) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
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| Samples (5)
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| Relations |
| SRA |
SRP009375 |
| BioProject |
PRJNA148601 |
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