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Series GSE39638 Query DataSets for GSE39638
Status Public on Mar 18, 2013
Title Genome-wide maps of 5hmC/5mC state in pluripotent and (T-)iPS induction cells.
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary We performed 5hmC/5mC DNA Immunoprecipitation followed high-throughput sequencing using the cell sample along the whole TSKM secondary reprogramming system. The TSKM 0D is the fibroblasts deried from TSKM-iPS mouse as the starting cells of the reprogramming.The intermediate cells is 3-days induced cells which are refered as TSKM 3D cells, and the final reprogrammed cells is the iPS cells with full pluripotency driven from this secondary system. We compared the profiling of 5-hydroxymethylcytosine and 5-methylcytosine modifications in these different cell lines. We found that: a widespread accompanying increase of 5hmC and 5mC at TSS and ES-active regulation regions followed by 5mC-5hmC pattern switch. Taking the advantage of the newly established TSKM secondary reprogramming system, the epigenetic remodeling and regulation mechanisms can be further investigated to advance our understanding of the epigenetic barriers and decipher the dynamic mechanism in somatic cell reprogramming.
Overall design Examination of 5-hydroxymethylcytosine/5-methylcytosine modifications in a Tet1-mediated secondary reprogramming system
Contributor(s) Gao Y, Chen J, Cai T, Gao S
Citation(s) 23499384
Submission date Jul 25, 2012
Last update date May 15, 2019
Contact name Tao Cai
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
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (6)
GSM973527 fibroblast 5hmC
GSM973528 fibroblast 5mC
GSM973529 TSKM-3D cell 5hmC
This SubSeries is part of SuperSeries:
GSE39639 Gene expression and 5hmC/5mC state in pluripotent and TSKM-iPS induction cells
BioProject PRJNA171321
SRA SRP014576

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

Supplementary file Size Download File type/resource
GSE39638_RAW.tar 9.2 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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