Extended Data Fig. 6: Isogenic differentiation and reprogramming system confirms transient-naive-treatment reprogramming enhances epigenome resetting.
From: Transient naive reprogramming corrects hiPS cells functionally and epigenetically
a) Phase contrast images showing the generation of fibroblast cells from MEL1 hESCs, where these cells were TRA160 negative and CD90 (Thy1) positive as shown by FACS analysis. Scale bar: 100 µm. b) Immunostaining of pluripotency markers NANOG and TRA160 for the MEL1 hESCs and the different Primed-hiPSC, TNT-hiPSC, and NtP-hiPSC lines derived from the MEL1-derived fibroblast-like cells, n = 2 independent experiments. Scale bar: 100 µm. c) Hierarchical clustering of 5 kb genome bin mCG/CG values for human tissues, cultured fibroblasts, and fibroblasts differentiated from hESCs. Somatic tissue WGBS data from Schultz et al. (2015)73. d) Upset plot showing the number of intersecting CG-DMRs detected between the hESC and hiPSC lines. e) Heatmap of CG DNA methylation levels in all lines in CG-DMRs detected between isogenic hESCs and Primed-hiPSCs, where r represents the replicate number. f) Histograms of the difference in CG DNA methylation level at CG-DMRs for Primed-hiPSCs, TNT-hiPSCs, and NtP-hiPSCs. Vertical dashed lines indicate the threshold of 0.2 (i.e. 20%) difference in CG DNA methylation level at CG-DMRs. g) Scatter plot of the relative CG DNA methylation difference in CG-DMRs for hiPSCs compared to hESCs (x-axis) and hiPSCs compared to fibroblasts (y-axis). Individual CG-DMRs are represented by individual points. h) Upset plot showing intersecting CG-DMRs detected for isogenic secondary fibroblast Primed-hiPSCs compared with CG-DMRs for primary fibroblast Primed-hiPSCs from this study and samples from previously published studies. i) Aggregate profile plot of CA methylation levels in hyper-methylated CH-DMRs.
