To compare hESCs with genetically matched hiPSC lines devoid of viral integrations, we generated hiPSCs from in vitro-differentiated hESCs using a non-integrating Sendai virus (SeV)-based reprogramming system19; SeV is an RNA virus that is diluted from infected cells in a replication-dependent manner, leaving no genetic footprint behind (Fig. 1A,B). We chose two well-characterized hESC lines, HUES2 and HUES320, for these experiments. We selected male hESC lines because female iPSCs can exhibit defects in X chromosome reactivation17,18, which might confound subsequent interpretations9,21.
