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| 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
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| 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.
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| 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.
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| 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
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| Department |
Genetics
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| Lab |
Nissim Benvenisty Lab, The Azrieli Center for Stem Cells and Genetic Research
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| Street address |
Givat Ram
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| City |
Jerusalem |
| ZIP/Postal code |
91904 |
| Country |
Israel |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (15)
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| This SubSeries is part of SuperSeries: |
| GSE61657 |
Coding mutations and loss-of-imprinting in human pluripotent cells derived by nuclear transfer and defined factors |
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| Relations |
| BioProject |
PRJNA261785 |
| SRA |
SRP047407 |
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