Analysis of the 54 676 probesets identified 20 550 unique transcripts expressed in iPSC and 20 718 in neuronally differentiated cells. We replicated five out of seven genes selected from our microarray in quantitative reverse transcriptase-polymerase chain reaction, supporting the validity of these results (Supplementary Table 1C). In the iPSC samples, 2538 transcripts were expressed at significantly different levels (Supplementary Figure 3A). KEGG pathway analysis identified one significant pathway in the iPSC, calcium signaling, n=39, P⩽2.5 × 10−2, Bonferroni correction. Many of these transcripts are associated with neuroplasticity and development, others with stress-activated pathways (Supplementary Table 2). Of the 20 718 transcripts identified in neuronally differentiated iPSC, 1835 transcripts were differentially expressed between groups (nominal P⩽0.05), but KEGG pathway analysis did not identify significantly altered pathways in the neuronal population. Additional analysis of the differentially expressed transcripts did not identify significant differences between BP vs control iPSC (distance=0.036, P⩽0.072), not surprisingly pooled iPSC vs neurons were significantly different (distance=0.174, P⩽0.012). Interestingly, BP and control neurons were also significantly different in their transcriptomes (distance=0.103, P⩽0.041); Supplementary Figure 3B.
