More Cit− clusters expressed PAX6 at D24 than later timepoints. DLL1, DLL3, HES6 and ASCL1 tended to be co-expressed in at least one Cit− cluster at each timepoint, perhaps indicating the emergence of intermediate progenitors. After D54, Cit− clusters expressed higher levels of MGE migration genes (i.e. ERBB4, CXCR4), and from D100 through D125, Cit− clusters expressed HOPX, AQP4 and S100B (Padj < 0.001 for Cit− cells at D100 and D125). Cit+ populations at D24 expressed DLX2, DLX5 and DLX6, indicating that these clusters were maturing interneurons (Padj <0.001, D24 Cit− vs. Cit+). D24 neurons did not express high levels of functional maturity genes, such as GRIA2, GRIA4, SST and RBFOX3, though these genes were expressed after D54 (Padj <0.001 D24 Cit+ vs. D54). Clusters that co-expressed OLIG1, OLIG2 and PCDH15 emerged after D100, indicating that oligodendrocyte precursors were present at late timepoints. For a detailed heatmap of all genes distinguishing D54 clusters, see figure S7. These data suggest that the cell types produced shift over time in terms of identity and maturation status with a temporal progression like that observed in vivo.
