The vast majority of mRNAs detected in these cultures was expressed at similar levels in either D398 or N398 DA neurons. The set of nAChR subunit mRNAs (Fig. 3C, green dots), as previously detected by qPCR (Fig. 1Q), was primarily within the 2-fold difference range (depicted by the vertical dashed lines), except for CHRNA5, which was relatively increased in D398 (8.7-fold higher, 0.02% FDR). qPCR assay (Fig. 1Q) indicated a similar difference although it was not statistically significant. Subjects were chosen for a homozygous major allele in rs880395 to exclude the potential effect on CHRNA5 mRNA levels observed previously37. Other groups of genes indicative of neuronal identity or maturity, including the gene ontology group members specific for dopaminergic differentiation (Fig. 3C, blue dots; also see Supplemental Fig. 3) were unaffected by the variation.
