Next, we applied gene set enrichment analysis (GSEA) to examine the expression of functionally related genes. iPSC clones from donor T42 (F-iPS2 and B-iPS1) showed downregulation of genes (25 of 61 genes; false discovery rate [FDR] = 0.002, normalized enrichment score [NES] = −2.2084) associated with Diamond-Blackfan anemia (DBA), which is functionally characterized by diminished erythroid precursor cells (Figure 5E) (Gazda et al., 2006). The finding was reproducible with two additional clones from the same donor (17 of 61 genes; FDR = 0.001, NES = −2.2400) (Figures S6A and S6B). Altogether, 15 overlapping genes were identified between these two sets (Figure S6C). We also asked whether differentiation potential and the noted differential gene expression differences between the lines can be linked to changes in methylation. We conducted additional comparisons between (T42F-iPS2, T42B-iPS1) and (T55F-iPS2, T55B-iPS1) for DMCs of 25% or more, and annotated to the TSS of the nearest protein coding gene. We found several genes that are likely involved in the differentiation of the lines to contain DMCs (Table S8). For example, we found that CpGs associated with NUCB2
