CG island reprogramming analysis was carried out as follows. CG-DMRs different between ES cells and differentiated cells were defined within the set of CG-DMRs identified comparing all analysed methylomes (see earlier), considering only CG-DMRs overlapping with CG islands. In particular, for each of these CG-DMR the mCG/bp levels in 20 equally sized bins was profiled in all cell types. DMRs with pooled mCG/bp levels different from differentiated and ES cell lines were identified (Wilcoxon test P value, < 0.01, and P value. > 0.05 between H1 and H9). Similarly, the set of reprogrammed CG-DMRs was identified by comparing pooled iPSC mCG profiles with the ES cell samples (Wilcoxon test P value. > 0.05).
