Given the different path to pluripotency and methods of differentiation, we looked at the expression of some genes/pathways that we and others have suggested might be different between hESCs and iPSCs such as genes involved in imprinting, cell cycle regulation, and reprogramming. Examination of imprinted genes which we thought may be different shows a small number of differences (Supporting Information Table 1). These included maternally expressed DLK1 and H19, and paternally expressed DLX5 and PEG3. It has been previously noted that the cell cycle in ESCs (pRb and p53 in particular) is regulated differently than in other somatic cell population [19]. Little difference at the transcriptome level was observed between the two iPSC lines and H9, suggesting that as cells transited to the iPSC state their cell cycle regulation changed appropriately. Likewise, the expression level of iPSC inducing genes (the three or four reprogramming factors) in the iPSC lines was comparable with H9 suggesting the exogenous induced genes had been silenced. Surprisingly, unlike other reports, we did not observe significant expression of fibroblast or mesodermal markers in undifferentiated iPSCs.
