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Series GSE34688 Query DataSets for GSE34688
Status Public on Jan 09, 2013
Title Induced Pluripotent Mesenchymal Stromal Cell Clones Retain Donor-Derived Differences in DNA Methylation Profiles
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Reprogramming of somatic cells into induced pluripotent stem cells (iPSC) is an epigenetic phenomenon. It has been suggested that iPSC retain some tissue-specific memory whereas little is known about inter-individual epigenetic variation of iPSC clones. In this study we have reprogrammed mesenchymal stromal cells (MSC) from human bone marrow by retrovirus-mediated overexpression of OCT-3/4, SOX2, c-MYC, and KLF4. Global DNA-methylation profiles of the initial MSC, MSC-derived iPSC (iP-MSC) and embryonic stem cells (ESC) were then compared using a high density DNA-methylation array covering more than 450,000 CpG sites. Overall, DNA-methylation patterns of iP-MSC and ESC were similar whereas some CpG sites revealed highly significant differences, which were not related to parental MSC. Furthermore, hypermethylation in iP-MSC versus ESC was particularly enriched in developmental genes as well as shore regions next to CpG islands indicating that these differences are not due to tissue-specific memory or random de novo methylation. Subsequently, we searched for CpG sites with donor-specific variation in MSC preparations. These “epigenetic fingerprints” were highly enriched in non-promoter regions and outside of CpG islands – and they were maintained upon reprogramming into iP-MSC. In conclusion, DNA methylation profiles of iP-MSC clones from the same donor were closely related despite heterogeneity of MSC. On the other hand, iP-MSC maintain donor-derived epigenetic differences. In the absence of isogenic controls for disease modeling applications, it would therefore be more appropriate to compare iPSC from different donors rather than a high number of different clones from the same patient.
Overall design 16 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
Contributor(s) Shao K, Koch C, Gupta MK, Lin Q, Lenz M, Laufs S, Denecke B, Schmidt M, Linke M, Hennies HC, Hescheler J, Zechner U, Saric T, Wagner W
Citation(s) 23032973, 25241740
Submission date Dec 23, 2011
Last update date Mar 22, 2019
Contact name Wolfgang Wagner
Phone +49 241 8088611
Organization name RWTH Aachen University
Department Helmholtz Institute for Biomedical Engineering
Lab Stem Cell Biology and Cellular Engineering
Street address Pauwelsstrasse 20
City Aachen
ZIP/Postal code 52074
Country Germany
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (16)
GSM853409 MSC donor2
GSM853410 MSC donor4
GSM853411 MSC donor5
BioProject PRJNA150297

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
GSE34688_Matrix_signals_GSM853409-GSM853422.txt.gz 42.5 Mb (ftp)(http) TXT
GSE34688_Matrix_signals_GSM979892-GSM979893.txt.gz 9.9 Mb (ftp)(http) TXT
GSE34688_RAW.tar 183.1 Mb (http)(custom) TAR
Processed data included within Sample table

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