Coding mutations and loss-of-imprinting in human pluripotent cells derived by nuclear transfer and defined factors
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE61657 | GEO | 2014/11/06
SECONDARY ACCESSION(S): PRJNA261784
REPOSITORIES: GEO
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-11-06 | E-GEOD-61657 | biostudies-arrayexpress
Project description: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. 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.
2014-11-06 | E-GEOD-61656 | biostudies-arrayexpress
Project description: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. Genome-wide DNA methylation profiling by Illumina Infinium HumanMethylation 450K Beadchip was performed on a total of 21 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, 6 iPSC lines and their parental adult fibroblast cell line (derived from a type 1 diabetic subject); as well as 7 control embryonic stem cell (ESC) lines.
2014-11-06 | E-GEOD-61461 | biostudies-arrayexpress
Project description: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.
2014-11-06 | GSE61656 | GEO
Project description: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.
2014-11-06 | GSE61461 | GEO
Project description:A panel of nine human cell lines comprising in vitro fertilization-derived embryonic stem cells (hESCs), nuclear-transfer embryonic stem cells (NT-ESCs; isogenic with the donor fibroblasts), induced pluripotent stem cells (iPSCs; isogenic with the donor fibroblasts) and parental dermal fibroblasts (hDFs) was profiled to compare the transcriptional and epigenetic landscapes that arise from different reprogramming routes. The four sequencing assays (transcriptome RNA-seq, MeDIP-seq for DNA methylation, H3K27ac ChIP-seq for active enhancer annotation and small RNA-seq for microRNA expression) were generated for the same set of donors so as to enable an integrative four-layer comparison. NT-ESCs and iPSCs largely recapitulate the core pluripotency network of hESCs but retain residual donor-cell signatures, and the method-of-derivation effect is most pronounced at the DNA methylation and microRNA layers.
2026-05-13 | GSE330334 | GEO
Project description:A panel of nine human cell lines comprising in vitro fertilization-derived embryonic stem cells (hESCs), nuclear-transfer embryonic stem cells (NT-ESCs; isogenic with the donor fibroblasts), induced pluripotent stem cells (iPSCs; isogenic with the donor fibroblasts) and parental dermal fibroblasts (hDFs) was profiled to compare the transcriptional and epigenetic landscapes that arise from different reprogramming routes. The four sequencing assays (transcriptome RNA-seq, MeDIP-seq for DNA methylation, H3K27ac ChIP-seq for active enhancer annotation and small RNA-seq for microRNA expression) were generated for the same set of donors so as to enable an integrative four-layer comparison. NT-ESCs and iPSCs largely recapitulate the core pluripotency network of hESCs but retain residual donor-cell signatures, and the method-of-derivation effect is most pronounced at the DNA methylation and microRNA layers.
2026-05-13 | GSE330335 | GEO
Project description:A panel of nine human cell lines comprising in vitro fertilization-derived embryonic stem cells (hESCs), nuclear-transfer embryonic stem cells (NT-ESCs; isogenic with the donor fibroblasts), induced pluripotent stem cells (iPSCs; isogenic with the donor fibroblasts) and parental dermal fibroblasts (hDFs) was profiled to compare the transcriptional and epigenetic landscapes that arise from different reprogramming routes. The four sequencing assays (transcriptome RNA-seq, MeDIP-seq for DNA methylation, H3K27ac ChIP-seq for active enhancer annotation and small RNA-seq for microRNA expression) were generated for the same set of donors so as to enable an integrative four-layer comparison. NT-ESCs and iPSCs largely recapitulate the core pluripotency network of hESCs but retain residual donor-cell signatures, and the method-of-derivation effect is most pronounced at the DNA methylation and microRNA layers.
2026-05-13 | GSE330336 | GEO
Project description:A panel of nine human cell lines comprising in vitro fertilization-derived embryonic stem cells (hESCs), nuclear-transfer embryonic stem cells (NT-ESCs; isogenic with the donor fibroblasts), induced pluripotent stem cells (iPSCs; isogenic with the donor fibroblasts) and parental dermal fibroblasts (hDFs) was profiled to compare the transcriptional and epigenetic landscapes that arise from different reprogramming routes. The four sequencing assays (transcriptome RNA-seq, MeDIP-seq for DNA methylation, H3K27ac ChIP-seq for active enhancer annotation and small RNA-seq for microRNA expression) were generated for the same set of donors so as to enable an integrative four-layer comparison. NT-ESCs and iPSCs largely recapitulate the core pluripotency network of hESCs but retain residual donor-cell signatures, and the method-of-derivation effect is most pronounced at the DNA methylation and microRNA layers.
2026-05-13 | GSE330333 | GEO
Project description: Not available
| S-EPMC6326833 | biostudies-literature