The 1,175 CG-DMRs identified between iPSCs and ES cells and the iPSC conserved CG-DMRs were profiled and confirmed in two previously reported ES cell DNA methylomes, HSF1 (ref. 23) and H9-Laurent (ref. 24) (Supplementary Fig. 14). Hierarchical clustering of the 1,175 CG-DMRs indicated that HSF1 and H9-Laurent ES cells are similar to H1 and H9. Lastly, we find that all of the iPSC hypermethylated CG-DMRs and 75% of the iPSC hypomethylated CG-DMRs are confirmed with respect to the two additional ES cell lines (P value < 0.05, as for H1 and H9).
