Fig. 2
hF clones are reprogrammed towards an embryonic pluripotent state by fusion with mouse ESCs. a Strategy used for examining Xi-gene reactivation during pluripotent reprograming of female hF clones. Isogenic clones with opposite XCI patterns (i.e. X1aX2i and X1iX2a) were fused with mESCs and RNA-sequencing was performed at 0, 4 and 6Â days after fusion. b Hierarchical clustering of transcription factor genes that are part of the human pluripotency-associated gene regulatory network [43] in hESC (i.e. H9), hF clones (i.e. clone 12 and 34) and at 0, 4 and 6Â days after mESC-fusion. Displayed values correspond to the expression level (rlog, regularised logarithmic transformation) that has been scaled by the mean expression of each gene across all samples. Expression levels were computed using RNA-seq reads that uniquely aligned to the human reference genome, but not to mouse. Sidebars highlight major clusters and are annotated with gene ontology. Red and green bars mark genes that are, respectively, upregulated or downregulated regulated upon cell fusion-mediated reprograming. Black bars mark clusters that are upregulated upon cell fusion but not in hESCs, or vice versa