(a) Genome browser view of Sall4 gene expression measured by RNA-Seq data (two biological replicates per timepoint). Bar graph insert depicts qRT-PCR measurements of Sall4 expression in two independent biological replicate reprogramming experiments (bars indicate mean values). (b) Scatterplot of RPKM gene expression values (n = 16,332 genes) for biological replicates 1 and 2 (iPS samples shown). (c) Pearson correlation (R2) values between RNA-Seq replicates (n = 16,332 genes) for all timepoints. (d) Genome browser views of the Ctsg and Rag genes with H3K4Me2 ChIPmentation (red) or ATAC-Seq (blue) profiles during reprogramming. Bar graphs below show gene expression dynamics (bars indicate mean values, n = 2). (e) qRT-PCR measurements of Nanog (top) and Sox2 (bottom) expression (mean values, n = 2) using primers that detect both mRNA and primary transcripts. Red rectangles indicate area depicted in smaller zoom-in graph on the right. (f) Normalized genome-wide H3K4Me2 (marking active chromatin) coverage per timepoint. (g) Fraction of Oct4 binding sites in PSCs overlapping with an ATAC-Seq peak (‘ATAC+’) during a representative reprogramming time course. Absolute numbers of sites are shown. (h) ATAC-Seq and (i) H3K4Me2 coverage profiles for Oct4 binding sites in PSCs inside (left, n = 821) and outside (right, n = 31,869) PSC superenhancers (SEs) during reprogramming. Error bars in the figure denote 95% CI.