Expression of many genes was highly correlated with differentiation status and pseudotime. For example, VIM, PDPN, and S1PR1 were expressed predominantly in progenitors, while interneuron genes such as SST, GAD1, and STMN2 gradually increased with differentiation status (Figure 3A, top panel. P < 10−100 for all genes described in this figure, see Table S2). Similarly, several genes showed significantly increased (BCAN, PTN, and C1orf6 (CROC4)) or decreased (FAM60A, CRABP2, and DLK1) expression with pseudotime (Figure 3A, right panel), likely representing a general program of development. Gene expression was often restricted by both differentiation status and pseudotime. In contrast to ZFP36L1, which was expressed in all progenitors (Cit−) populations, COL2A1 and AQP4 were confined to early- and late-stage progenitors, respectively (Figure 3B, left panels). Similarly, while DCX expression increased with differentiation stage, LHX8 was maximally expressed in early (e.g. newly generated) pseudotime neurons, whereas SST expression was highest in late (e.g. more mature) pseudotime neurons (Figure 3B, right panels). To verify these results, we compared gene expression changes correlated with pseudotime for our in vitro cells to gene expression patterns observed
