Figure 3: Gene expression differences in iPSC derived DA neurons exhibit patterns of differential response.

(A) Hierarchical clustering indicates that D398 and N398 DA cultures were more similar to mDA cultures than to iPSC or iPSC-derived NSC (NSC0), or NSC differentiating into glutamatergic neurons (5 days of differentiation, NSC5). The dendrogram shows relative distances (based on the Jenson-Shannon divergence metric) for the top 500 genes varying by group. (B) Expression patterns for genes characteristic of midbrain DA neurons. The mean FPKM is plotted ± the 95% confidence interval, n = 3/group. (C) RNAseq volcano plot. The horizontal axis shows the log₂ fold-change, comparing N398 to D398. The vertical axis shows the false discovery rate (FDR) as the −log₁₀ of the value. Points are plotted as individual genes not significantly different (grey dots) or significantly different (black dots) at 1% FDR (horizontal dashed line) and at least 2-fold different (vertical dashed lines). Colored dots indicate the nAChR receptor neuronal markers (green), GO dopamine differentiation genes (blue) and differentially-regulated genes belonging to the significantly-enriched pathways relatively increased in N398 (red). (D) Pathway (KEGG) analysis identifies three functional groups as enriched in the list of genes increased in N398. Bar colors indicate enrichment in N398 (red) or D398 (blue). The bar length indicates the FDR, and the color intensity (alpha) indicates the number of genes enriched. See Supplemental Table 4 for additional functional analyses.