To comprehensively characterize hSS and hCS, we performed single cell transcriptional profiling at day 105 of differentiation using stochastic barcoding13 (n= 11,838 cells from hCS and hSS; BD™ Resolve system; Fig. 1i). Clustering of cells isolated from either hCS or hSS using the t-Distributed Stochastic Neighbor Embedding (t–SNE)14 revealed a separation of the two conditions. Neurons expressing STMN2 were localized on the upper left of the t–SNE space, whereas progenitors and mitotically active cells were distributed in the lower right (Extended Data Fig. 2a–c). Further examination identified several subdomains in hCS (Fig. 1j, Extended Data Fig. 2d), including a group of glutamatergic neurons (VGLUT1+) expressing the cortical layer markers TBR1, FEZF2, CTIP2; two groups of intermediate progenitors expressing TBR2, INSM1, HES6; and a group of dorsal progenitors expressing LHX2, PAX6 and GLAST1 that also encompass HOPX+ outer radial glia-like cells. In contrast, hSS included a cluster of ventral neural progenitors, a group of GABAergic cells expressing DLX1, GAD1, SLC32A1, SCG2, SST, and a small group of oligodendrocyte progenitors (OLIG2, SOX10) (Supplementary Table 3; Extended Data Fig. 2e–m). Astroglia from both
