RNA-Seq results confirmed the qPCR findings of lower expression of chr4p12 GABAA genes in neural cell cultures from Cluster 1 vs. Cluster 2 (Figure 4B 2–5) (GABRG1 F=22.2, df=1,7.6, p=0.002; GABRA2 F=7.7, df=1,8.2, p=0.024; GABRA4 F=15.7, df=1,7.8, p=0.004; GABRB1 F=6.0, df=1,8.5, p=0.039). There was no significant difference (p>0.50) in the expression of genes encoding GABAA subunits located on chromosomes 5q34 (GABRG2, GABRB2), 15q12 (GABRB3), or 1p36 (GABRD) (Figure 4C 1–4), or in the expression of the cation-chloride transporters NKCC1 (encoded by SLC12A2) and KCC2 (encoded by SLC12A5) (Figure 4C 5–6), which regulate the intracellular chloride concentration during development and determine whether GABA is an inhibitory or excitatory neurotransmitter (Stein et al., 2004). Similarly, with the exception of GABRA2 and GABRB1 genes, there were no significant differences between Cluster 1 and Cluster 2 neural cultures in the level of RNA for a panel of 74 neural patterning genes used by other investigators (Brennand et al., 2014) to compare developmental characteristics of iPSC-derived neural cultures (Supplemental Table 1). These results suggest that the two clusters had a similar degree of neuronal maturation
