Cells from individual subjects were distinguished by expressed SNPs [41], and sequencing reads from each subject were combined to create a “pseudo-bulk” analysis, treating each subject and treatment condition as replicates. Comparing the untreated AF group with the untreated UN group, we identified 797 up-regulated genes, and 596 downregulated genes (Fig. 1D; Supplementary Table 3). Examining the results for differences by sex instead of KCNJ6 haplotype identified only 6 genes, 4 of which are encoded on X or Y, indicating that the sex of the samples did not substantially contribute to gene expression differences. Gene ontology analysis of the downregulated genes (Fig. 1E; Supplementary Tables 4, 5) predicts several biological processes associated with nervous system development, axonal transport, and trans-synaptic signaling. By grouping enriched gene ontology terms by their parent terms (Supplementary Fig. 3), the major themes in the downregulated genes (Supplementary Table 5) are synaptic signaling and neuro projection morphogenesis. Up-regulated genes (Supplementary Table 4) predict functions associated with protein targeting within the cells, catabolic metabolism, and nonsense-mediated decay. KCNJ6 mRNA trended lower in untreated AF than in UN
