In further support of the notion that genetic background profoundly influences transcriptional patterns in pluripotent cell lines, we found that DEGs that distinguish our HUES2-derived and HUES3-derived cell lines account for more transcriptional variation among our 30 unmatched hESCs and hiPSCs than do all genes or DEGs that distinguish our isogenic hESCs and hiPSCs or SeV-infected and uninfected hESCs (Fig. 5F). Taken together, these meta-analyses suggest that the main transcriptional differences between genetically unrelated hESC and hiPSC lines are primarily driven by genetic background rather than cellular origin or reprogramming method.
