To eliminate donor-derived variability in methylation profiles, we compared F- and B-iPSCs for each donor. We identified the largest number of DMCs for isogenic iPSCs derived from donor T42 (9,057 = 3.2%) followed by T55 (2,620 = 0.92%), T14 (2,142 = 0.76%), and T53 (795 = 0.28%) (Figure 2A). Of these, an average of 66% were donor-unique DMCs, with the exception of T42-derived F- and B-iPSC lines where 84% of the DMCs were unique for that genetic background (Figure 2A). We identified 34 DMCs common to all four donors (Figure S2E). Notably, eight of these common DMCs are in the TCERG1L locus (Lister et al., 2011, Wang et al., 2013) (Figure 2B). The fraction of CpGs differentially methylated between F- and B-iPSCs is lower than between two different hESC lines (H1 and H9) (Bock et al., 2011) (Figure 2A). This again suggested that F- and B-iPSCs are highly similar to each other. To quantify both abnormal methylation and somatic memory phenotypes we compared the methylation signatures of hESCs, isogenic iPSC lines, and somatic parental cells using k-means clustering (Figure S3).
