differing between Q1SA and Q3SC were in common with the Q1SA versus Q3SA comparison (Figure 4B), even though the latter compared two different ATM−/− cell lines. Nayler et al. (2012) identified 7,920 genes as significantly different in A-T iPSC compared with wild-type cells using the same selection criteria. This list translated to 7,402 unique RefSeq transcript identifiers, and only 50 of these overlapped with the 206 Q3SA versus Q3SC transcripts found here. Three hundred sixty-four of Nayler’s selected transcripts overlapped with the broader Q1SA versus Q3SC list, again indicating that comparisons between isogenic pairs are distinct from those between cell lines with different genetic backgrounds.
