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 and 450K DNA Methylation BeadChips (27K and 450K DNA Methylation array) as well as the Illumina HT12v3 Gene Expression BeadArray. These platforms interrogate DNA methylation at 27,578 CpG sites associated with ~14,500 well-annotated genes (27K DNA Methylation array), >450,000 CpG sites associated with both coding and non-coding genes (450K DNA Methylation array) (Sandoval et al., 2011), and the expression of over 30,000 mRNA transcripts (HT12v3). A summary of samples and analyses performed are detailed in Table S1.
