In Fig. 4a each of the 11 CG-DMRs consistently hypermethylated in the 5 iPSC lines was profiled for both mCG and the H3K27me3 histone mark throughout the CG-DMR and equivalent upstream and downstream genomic regions divided into 30 equal-length bins. For DNA methylation, for each bin in each sample the total number of methylated/(methylated+unmethylated) reads was determined over the whole set of considered CG-DMRs. Final profiles were normalized by dividing them by their maximum value. For the H3K27me3 histone modification ChIP-Seq reads, RPKM values were determined in each CG-DMR and normalized to the average of the upstream/downstream flanking region RPKM values.
