To annotate functions to genes regulated during differentiation, enrichment analysis of DEGs was performed. The GO analysis of DEGs demonstrated that the progressive differentiation from NP to E and L neurons was associated primarily with genes involved in cell cycle regulation and neurogenesis in both BPD and control populations (S4 and S5 Tables). There was a robust alteration in the expression of genes associated with neuronal differentiation and specification as exemplified by the axonal guidance signaling pathway (defined by Ingenuity Pathway Analysis) upon differentiation from iPSC to NP to E and L neurons (Fig 4C). Importantly, the patterns of gene expression were similar in RNAs isolated from BPD and control donors. Collectively, these data demonstrate that our differentiation paradigm was robust and BPD iPSCs differentiated similarly to the control iPSCs.
