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Series GSE61656 Query DataSets for GSE61656
Status Public on Nov 06, 2014
Title Coding mutations and loss-of-imprinting in human pluripotent cells derived by nuclear transfer and defined factors [RNA-Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Human pluripotent stem cells can be derived from somatic cells by forced expression of defined factors, and more recently by nuclear-transfer into human oocytes, revitalizing a debate on whether one reprogramming approach might be advantageous over the other. Here we compared the genetic and epigenetic stability of human nuclear-transfer embryonic stem cell (NT-ESC) lines and isogenic induced pluripotent stem cell (iPSC) lines, derived from the same somatic cell cultures of fetal, neonatal and adult origin. Both cell types shared similar genome-wide gene expression and DNA methylation profiles. Importantly, NT-ESCs and iPSCs have comparable numbers of de novo coding mutations but significantly higher than parthenogenetic ESCs. Similar to iPSCs NT-ESCs displayed clone- and gene-specific aberrations in DNA methylation and allele-specific expression of imprinted genes, similarly to iPSCs. The occurrence of these genetic and epigenetic defects in both NT-ESCs and iPSCs suggests that they are inherent to reprogramming, regardless of the underlying technique.
Overall design RNA sequencing analysis was performed on a total of 12 human cell lines, including: an isogenic set of 3 nuclear-transfer embryonic stem cell (NT-ESC) lines, 2 RNA-reprogrammed induced pluripotent stem cell (iPSC) lines and their parental neonatal fibroblast cell line; an isogenic set of 1 NT-ESC line, 3 iPSC lines and their parental adult fibroblast cell line (derived from a type 1 diabetic subject); as well as 1 control embryonic stem cell (ESC) line.
Contributor(s) Johannesson B, Sagi I, Yamada M, Benvenisty N, Egli D
Citation(s) 25517467
Submission date Sep 23, 2014
Last update date May 15, 2019
Contact name Ido Sagi
Organization name The Hebrew University of Jerusalem
Department Genetics
Lab Nissim Benvenisty Lab, The Azrieli Center for Stem Cells and Genetic Research
Street address Givat Ram
City Jerusalem
ZIP/Postal code 91904
Country Israel
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (15)
GSM1510127 BJ fibroblasts
GSM1510128 1018 fibroblasts
GSM1510129 BJ-NT-ES-5 rep 1
This SubSeries is part of SuperSeries:
GSE61657 Coding mutations and loss-of-imprinting in human pluripotent cells derived by nuclear transfer and defined factors
BioProject PRJNA261785
SRA SRP047407

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Supplementary file Size Download File type/resource
GSE61656_Samples_FPKM.txt.gz 1.5 Mb (ftp)(http) TXT
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