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

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.