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Series GSE81790 Query DataSets for GSE81790
Status Public on May 24, 2016
Title Regulation of DNA methylation landscape in human somatic cell reprogramming by miR-29 family (illumina 450K)
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Reprogramming to pluripotency after overexpression of OCT4, SOX2, KLF4 and MYC is accompanied by global genomic and epigenomic changes. Histone modification and DNA methylation states in iPSCs have been shown to be highly similar with embryonic stem cells (ESCs). However, epigenetic differences still exist between iPSCs and ESCs. In particular, aberrant DNA methylation states found in iPSCs are a major concern for using iPSCs in a clinical setting. Thus, it is critical to find factors that regulate DNA methylation states in reprogramming. Here, we found that the miR-29 family is an important epigenetic regulator during human somatic cell reprogramming. Our global DNA methylation and hydroxymethylation analysis shows that DNA demethylation is a major event mediated by miR-29a depletion during early reprogramming, and that iPSCs derived from miR-29a depletion are epigenetically closer to ESCs. Our findings uncover an important miRNA-based approach to generate clinically robust iPSCs.
 
Overall design Bisulphite converted gDNAs of D551 fibroblasts transduced for 3 days with overexpression of DNMTs, TETs, TDG and OSKM or miR29a/b/c and control sponge were hybridized into Illumina Infinium HumanMethylation 450K Beadchip.
 
Contributor(s) Hysolli E, Tanaka Y, Park I
Citation(s) 27373925
Submission date May 23, 2016
Last update date Mar 22, 2019
Contact name Eriona Hysolli
E-mail eriona.hysolli@gmail.com
Organization name Yale University
Department Genetics
Lab In-Hyun Park
Street address 10 Amistad Street
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (14)
GSM2175438 miR29a/b/c sponge
GSM2175439 Ctrl sponge
GSM2175440 Empty vector
This SubSeries is part of SuperSeries:
GSE81794 Regulation of DNA methylation landscape in human somatic cell reprogramming by miR-29 family
Relations
BioProject PRJNA322544

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
GSE81790_RAW.tar 296.1 Mb (http)(custom) TAR (of IDAT)
GSE81790_matrix_signal_intensities.txt.gz 112.4 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data is available on Series record
Processed data included within Sample table

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