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Series GSE53060 Query DataSets for GSE53060
Status Public on Jul 08, 2014
Title Epigenetic and transcriptional aberrations in human pluripotent stem cells reflect differences in reprogramming mechanisms [methylation array]
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Human pluripotent stem cells hold great potential for regenerative medicine, but existing cell types have imitations. Human embryonic stem cells derived from fertilized embryos (IVF-ESCs) are considered the “gold standard”, but are allogeneic to potential recipients. Autologous induced pluripotent stem cells (iPSCs) can be produced from somatic cells by forced expression of pluripotency-associated factors, but are prone to genetic and epigenetic aberrations. To determine whether accumulation of such aberrations is intrinsic to somatic cell reprogramming, or secondary to the reprogramming method, we employed an alternative approach by somatic cell nuclear transfer (SCNT). SCNT-based reprogramming to NT-ESCs is mediated by factors present in oocyte’s cytoplasm, thus mimicking early embryogenesis. We generated genetically matched pluripotent stem cells and conducted genome-wide genetic, epigenetic and transcriptional analyses. We discovered that unlike iPSCs, NT-ESCs have a low burden of de novo copy number variations (CNVs), reflecting superior maintenance of genetic stability. Moreover, DNA methylation and transcriptome profiles of NT-ESCs corresponded closely to those of IVF-ESCs. In contrast, iPSCs harbored methylation abnormalities including residual CpG methylation typical of parental fibroblasts, suggesting incomplete reprogramming. We conclude that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT with the potential to satisfy the clinical requirements for cell replacement therapies.
Overall design Bisulphite converted DNAs of two IVF-ESCs, two sendai produced iPSC lines, two retro-virus produced iPSC lines, four NT-ESCs, and the parental fibroblast were hybridized to the Illumina Infinium HumanMethylation 450K Beadchip
Contributor(s) Morey RE
Citation(s) 25008523
Submission date Dec 06, 2013
Last update date Mar 22, 2019
Contact name Robert E Morey
Organization name UCSD
Department Pathology
Lab Parast
Street address 2880 Torrey Pines Scenic Dr
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (11)
GSM1281444 Sample1_NT1
GSM1281445 Sample2_NT2
GSM1281446 Sample3_NT3
This SubSeries is part of SuperSeries:
GSE53096 Epigenetic and transcriptional aberrations in human pluripotent stem cells reflect differences in reprogramming mechanisms
BioProject PRJNA230786

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
GSE53060_RAW.tar 183.1 Mb (http)(custom) TAR
GSE53060_signals.txt.gz 38.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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