Fig. 4
Epigenetic memory of isogenic human iPSCs from six organs a Illustration describing the experimental setup for reprogramming. OSKM, reprogramming factors POU5F1, SOX2, KLF4, MYC. b Bright-field pictures of the primary cells (first row, scale bar 50 µm) and the iPSC colonies of clone #1 (second row, scale bar 1 mm) from the six organs. The iPSCs (clones #1) were immunostained for POU5F1 and TRA-1-81 (third row, scale bar 100 µm) and NANOG and SSEA4 (fourth row, scale bar 100 µm). For the single channels and the immunostaining of clones #2 see Supplementary Fig. 4a. c Real-time quantitative PCR analysis of the 12 iPSCs for endogenous SOX2, endogenous OCT4 and NANOG. NKX2.5eGFP/w hESCs were used as positive and fetal skin as negative control. Each bar represents the mean of three technical replicates ± standard deviation. d Violin plots depicting the distribution of the DNA methylation (beta values) of the 12 iPSCs and their isogenic organ of origin. e Hierarchical clustering of the 12 iPSCs and their isogenic organ of origin based on the DNA methylation profiles. f Heatmap of uniquely hypermethylated (top) and hypomethylated (bottom) CpGs in the 12 iPSCs compared to the six organs of origin with a beta value difference of > 0.2 or < 0.2, respectively. See also Supplementary Data File 5. g Heatmap depicting uniquely hypermethylated (top) and hypomethylated (bottom) CpGs in the brain triplet (two iPSC clones and brain) compared to the five triplets with a beta value difference of > 0.2 or < 0.2, respectively. The genic location and gene identity are provided
