CG-DMR reprogramming analysis was carried out as follows. CG-DMRs aberrant in iPSCs and like or unlike parental cells were defined within the set of 1,175 CG-DMRs identified comparing all ES cell and iPSC samples. In particular, for each of these CG-DMR the mCG/bp levels in 20 equally sized bins was profiled in all cell types. CG-DMRs aberrant in each iPSC line were identified comparing their mCG/bp to both H1 and H9 ES cell lines (two-tailed Wilcoxon test P value < 0.05 for both, and P value. > 0.01 between H1 and H9). Hypermethylated and hypomethylated CG-DMRs were identified in the same way but using a one-tailed test. Memory and iPSC-specific (iDMR) CG-DMRs were identified comparing the mCG/bp density between each iPSC and its parental line (Wilcoxon test P value > 0.01 and P value < 0.01, respectively).
