Dataset Information

Multi-omic profiling of human pluripotent cells derived by nuclear transfer and defined factors (MeDIP-seq)

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE330334 | GEO | 2026/05/13

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description: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. 16 matched samples, two IVF-ESCs, five sendai produced iPSC lines, two retro-virus produced iPSC lines, four NT-ESCs, the parental fibroblast line, and the sperm and oocyte donor were genotyped using the Illumina Omni5, which interrogates 4.3 million SNPs across the human genome. Additionally, matched samples from a patient with Leigh syndrome, a NT-ESC line, three iPSC lines, and the parental fibroblast line were genotyped using the Illumina Omni5.

Dataset Information

Multi-omic profiling of human pluripotent cells derived by nuclear transfer and defined factors (MeDIP-seq)

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets