We then used embryoid body (EB) analysis to investigate the impact of somatic cell type- and donor-dependent characteristics on the spontaneous differentiation potential of F- and B-iPSCs. Correlation clustering of global gene expression showed no specific clustering of EBs (Figure S5A). Although it has been reported that iPSC lines preferentially differentiate into the lineage of the cell type of origin, we were unable to detect any differentiation bias toward any embryonic germ layer of specific lineage (data not shown) or the hematopoietic lineages in particular (Figure S5B) (gene list according to Bock et al., 2011). Both F- and B-iPSC lines are able to differentiate into derivatives of all three embryonic lineages despite the cell type of origin. To examine whether EBs showed donor-specific differentiation propensities, we analyzed the expression of 167 genes that separated iPSC lines from different donors (Table S6) and found that spontaneously differentiated EBs maintained this difference (Figure 3A). Together, these results indicate that the differences in gene expression at the iPSC stage are maintained through differentiation.
