Experimental design and comparison of DNA methylation profiles of iPSCs and ESCs. A) Scheme showing the experimental design. Cells were treated identically and 25 days post-infection, colonies were picked randomly and maintained in culture for 6 passages. We profiled DNA methylation during early passage iPSCs to reduce the confounding contribution of negative selection during culture conditions , which may mask the differences between these 2 reprogramming factor combinations. B) Pair-wise plot shows that all iPSC methylomes are similar to ESC methylomes and significantly different from fibroblast methylomes. The raw methylation data was normalized and background-subtracted using the Illumina Genome Studio software. Intensity values were converted to beta-values where the value of 0 represents unmethylated and the value of 1 represents fully methylated. Fib stands for fibroblasts. C) Boxplot of the percentages of highly methylated (red) and lowly methylated (blue) CpGs in fibroblasts, ESCs, Y-iPSCs and T-iPSCs show that their overall levels in iPSCs are largely similar to those in ESCs. Hypermethylated CpGs are defined as those with values > 0.7 and hypomethylated CpGs are defined as those with values < 0.3. Hyper and Hypo stand for hypermethylated and hypomethylated, respectively. D) Boxplot of the percentages of highly methylated (red) and lowly methylated (blue) CpGs in fibroblasts, Y-iPSCs and T-iPSCs that are significantly different from ESCs (defined as those with difference in methylation > =0.2) show that only a small proportion of the CpGs in iPSCs are different from those in ESCs. E) Boxplot made as in Figure 1D but restricted to only those CpGs that change their methylation state from fibroblasts to ESCs. CpGs hypomethylated in fibroblasts but hypermethylated in ESCs (green) are more likely to be significantly different in iPSCs than CpGs that are hypermethylated in fibroblasts and hypomethylated in ESCs (yellow).