Next, we determined the potential overlap between DEGs identified within our isogenic and unmatched hESC/hiPSC lines, and two previously reported sets of DEGs8,10. There was little to no overlap between DEGs discovered by independent laboratories (Fig. 5C and Supplementary Fig. 4B) and these DEGs could not distinguish hiPSC and hESC lines from the respective other data sets using supervised clustering (Supplementary Fig. 4C-I). Only two of our 49 DEGs (MT1E, S100A14) and two of our 8 iDEGs (IRX2 and DPP10) overlapped with DEGs reported in ref. 10. Collectively, these data support the view that other parameters, such as reprogramming method, genetic background or sex, account for the majority of previously reported transcriptional differences between hESCs and hiPSCs.
