In order to study the effects of reprogramming and time in culture on epigenetic stability, we generated 11 hiPSC clones from fibroblasts and 4 hiPSC clones from chondrocytes. We collected samples for analysis from the parental fibroblast and chondrocyte populations, early passage samples from both chondrocyte and fibroblast-derived hiPSC clones and late passage samples from the fibroblast derived hiPSC clones. All clones were shown to be pluripotent as demonstrated by immunocytochemistry for pluripotency markers, in vitro differentiation, teratoma formation, silencing of reprogramming factors and PluriTest (Muller et al., 2011) (Figure S4, Table S1). For these analyses, we identified 214 CpGs on the 450K DNA Methylation array that had DNA methylation patterns consistent with gametic imprinting according to patterns observed in hydatidiform mole, parthenogenetic hESC and tissue samples (Experimental Procedures, Table S5B). DLGAP2, KCNK9, MEG3, MKRN3, ANKRD11 and PEG3/ZIM2, were hypermethylated in all hiPSC clones relative to the parental samples, suggesting that these aberrations occurred during reprogramming (Figure 4B).
