To analyze differences in expression profiles resulting solely from the cell type of origin, we grouped iPSC lines according to their parental cell type into two groups (F- and B-iPSCs). The reproducibility-optimized test statistic (Elo et al., 2008) and significance analysis of microarrays (SAM) (Tusher et al., 2001) identified only two differentially expressed genes (TCERG1L and COL22A1) between the iPSC groups. Using a separate statistical test, two-group empirical Bayes method (BH, p < 0.05) (Smyth, 2004), we identified only TCERG1L as a gene expressed significantly higher in B-iPSCs than in F-iPSCs. To increase the power of analysis, we used an arbitrary fold-change (FC) cutoff of >1. We subsequently identified 13 differentially expressed genes between F- and B-iPSC groups. However, unsupervised hierarchical clustering of all iPSC lines did not separate them into two groups according to the cell type of origin (Figures S2A and S2B). This suggests that the detected differences between iPSC lines were not due to different tissues of origin.
