Although global patterns of DNA methylation in the CG context appeared very similar between ES cells and iPSCs (Figs 1 and 2), a comprehensive analysis of CG DNA methylation between all ES cell and iPSC lines identified 1,175 differentially methylated regions (CG-DMRs) that were differentially methylated in at least one iPSC or ES cell line (1% false discovery rate (FDR); Fig. 3a and Supplementary Table 2) and in total comprised 1.68 Mb ranging from 1–11 kb in length. Importantly, identification of CG-DMRs between the H1 and H9 ES cells with the same criteria (1% FDR) provided no results (see Supplementary Methods for details). Whereas mCG patterns within each category of cells (ES cell, iPSC, somatic) were generally consistent and distinct from the cells in each other category, individual cell lines showed some variability.
