Gene expression analysis for undifferentiated cells and cells differentiated with BMPs for 7 and 14 days. The combined expression of endogenous and exogenous (derived from viral vectors) pluripotency markers OCT3/4 and NANOG was significantly different between all undifferentiated cell lines; iPSCs had higher expression relative to hESCs. At day 7 of differentiation, iPS(IMR90) and HSF1 had higher expression of OCT3/4 and iPS(IMR90) had higher expression of NANOG compared with other cell lines; however, at day 14, the levels decreased to the similar levels between all cell lines. As a further indication of differentiation, the expression of KRT7 (trophectodermal marker), GATA6 (endodermal marker), ACTC (mesodermal marker) and NCAM1 (ectodermal marker) increased similarly for all cell lines upon differentiation, although at day 7 the expression of GATA6 was significantly higher in HSF1 cells relative to iPS(IMR90) cells and at day 14 the expression of KRT7 and NCAM1 was higher in iHUF4 cells relative to H9 or HSF1 cells, respectively. In undifferentiated cells, iPS(IMR90) had significantly higher expression of KRT7 relative to H9 and iHUF4, and GATA6 relative to all other cell lines. The expression of ACTC was significantly higher in both undifferentiated iPSCs relative to hESCs, but the expression of NCAM1 was higher in H9 cells relative to HSF1 and iPS(IMR90) and in iHUF4 cells relative to HSF1 cells. The expression of early germ cell markers IFITM1, PELOTA and PRDM1A indicate the potential of all cell lines to differentiate toward the germ cell lineage, with similar expression levels between hESCs and iPSCs. However, the expression of IFITM1 at day 7 and PELOTA in undifferentiated cells was significantly higher in iPSCs relative to hESCs. In addition, the expression of IFITM1 in undifferentiated iPS(IMR90) cells was significantly higher relative to other cell lines, and in HSF1 relative to H9 and iHUF4 cells. The expression on PRDM1A was significantly higher at day 7 in HSF1 cells relative to H9 and iPS(IMR90) cells. Values are normalized to expression levels of two housekeeping genes, GAPDH and RPLPO, and results are shown as fold difference relative to undifferentiated H9 cells using the log scale. Statistical testing was performed comparing the values of different cell lines within a time group; undiff, day 7, and 14, for each gene separately. Error bars indicate SD between three technical replicates. *P < 0.05, one-way ANOVA.