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Series GSE57179 Query DataSets for GSE57179
Status Public on Jul 02, 2014
Title Epigenetic and transcriptional aberrations in human pluripotent stem cells reflect differences in reprogramming mechanisms
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Human pluripotent stem cells hold great potential for regenerative medicine, but available cell types have important limitations. While embryonic stem cells derived from fertilized embryos (IVF-ESCs) are considered the 'gold standard' of pluripotency, they are allogeneic to potential recipients. Autologous induced pluripotent stem cells (iPSCs) are prone to epigenetic and transcriptional aberrations. To determine whether accumulation of such aberrations is intrinsic to somatic cell reprogramming or secondary to the reprogramming method, we generated a genetically matched collection of human IVF-ESCs, iPSCs, and ESCs derived by somatic cell nuclear transfer (SCNT; NT-ESCs), and subjected them to genome-wide genetic, epigenetic and transcriptional analyses. SCNT-based reprogramming is mediated by the full complement of oocyte cytoplasmic factors, thus closely recapitulating early embryogenesis. NT-ESCs and iPSCs derived from the same somatic donor cells contained comparable numbers of de novo copy number variations (CNVs), suggesting that the two reprogramming methods may not differ significantly in mutagenic or selective pressure. On the other hand, the DNA methylation and transcriptome profiles of NT-ESCs corresponded very closely to those of IVF-ESCs, while iPSCs differed markedly from IVF-ESCs and harbored residual DNA methylation patterns typical of parental fibroblasts, suggesting incomplete reprogramming. We conclude that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT and are therefore ideal candidates for cell replacement therapies.
Overall design Whole-genome single-base resolution methyl-C sequencing collected from a variety of Human pluripotent cells
Contributor(s) O'Neil RC, He Y, Schultz MD, Nery JR, Castanon R, Ecker JR
Citation(s) 25008523
Submission date Apr 30, 2014
Last update date May 15, 2019
Contact name Joseph R Ecker
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (11)
GSM1385973 SCNT-1
GSM1385974 HDF
GSM1385975 HESO-7
BioProject PRJNA247457
SRA SRP041984

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Supplementary file Size Download File type/resource
GSE57179_RAW.tar 47.0 Gb (http)(custom) TAR (of TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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