E-GEOD-39638 - Genome-wide maps of 5hmC/5mC state in pluripotent and (T-)iPS induction cells

Released on 18 March 2013, last updated on 24 March 2013
Mus musculus
Samples (6)
Protocols (4)
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. Examination of 5-hydroxymethylcytosine/5-methylcytosine modifications in a Tet1-mediated secondary reprogramming system
Experiment type
methylation profiling by high throughput sequencing 
Tao Cai <caitao@nibs.ac.cn>, Jiayu Chen, Shaorong Gao, Yawei Gao
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-39638.idf.txt
Sample and data relationshipE-GEOD-39638.sdrf.txt
Processed data (1)E-GEOD-39638.processed.1.zip