Although genetic background accounted for most transcriptional differences among the analyzed pluripotent cell lines, we noticed that hESCs clustered with each other and separately from hiPSCs within a given background, suggesting subtle but consistent transcriptional differences that reflect distinct cellular origins (Fig. 2D). To identify any DEGs that distinguish hESC from hiPSC lines independent of SeV infection and genetic background, we compared transcriptional profiles of hiPSC lines with those of genetically matched hESC GFP lines. This analysis revealed that 52 and 91 genes were up- and down- regulated, respectively, in hiPSC lines derived from the HUES2 background, whereas 77 and 426 genes were up- and down-regulated in hiPSC lines derived from the HUES3 background, respectively. Forty-nine genes were commonly dysregulated in both genetic backgrounds (Fig. 3A). Considering the good depth of our RNA-seq data (~40 million mapped reads per sample on average) (Supplementary Fig. 2E), it is highly unlikely that this small number of DEGs was due to low sensitivity. As expected, the 49-DEG signature reliably separated our hiPSC lines from our hESC lines (Fig. 3B).
