Previous studies of epigenetic stability and variation in hPSCs have been limited in scope and resolution. Most have used allele-specific expression of selected imprinted genes (Adewumi et al., 2007; Frost et al., 2011; Kim et al., 2007; Rugg-Gunn et al., 2007), restriction landmark genome scanning of a small portion of the genome (Allegrucci et al., 2007), or XIST expression to infer the overall epigenetic status of a small number of hESC samples (Hall et al., 2008; Shen et al., 2008; Silva et al., 2008). To obtain a comprehensive view of hPSC-specific epigenomic patterns, we collected 136 hESC and 69 hiPSC samples representing more than 100 cell lines for analysis. In order to establish expected variation in human tissues, we collected 80 high-quality and well-replicated samples representing 17 distinct tissue types from multiple individuals. Finally, we selected 50 additional samples from primary cell lines of diverse origin to control for any aberrations that may arise as a general, non-hPSC-specific, consequence of in vitro manipulation. With these samples, we performed genome-wide DNA methylation and mRNA expression profiling using the Illumina Infinium 27K
