Comparison with the published single-cell transcriptome from human brain tissues (Darmanis et al., 2015) further confirmed that 10 neuronal clusters resemble the differentiated neurons (Figure S4B). In addition, three non-neuronal clusters, which are mainly derived from early-stage of orgadnois, were significantly correlated with neural progenitor cells (NPC1-3). Cell cycle and chromatin-related genes were enriched and pluripotent genes were completely downregulated in NPCs (Figure S4A and S4C). Interestingly, we noticed that the IP marker TBR2 may also express in differentiated neurons, as revealed by its co-expression with TBR1 (Figure S4D). Four non-neuronal clusters were exclusively derived from hCOs. Subplate cell identity (PCP4+ and PLS3+) was present in three of them (SP1-3) (Figure 5D and 5H), and the other cluster displayed significant enrichment of cilium development and was annotated as ependymocytes (EP). The other six non-neuronal clusters show no functional characters. These clusters displayed weak enrichment for NPC character, but lacked mature neuronal identity (Figure S4B), and thus, were classified as intermediate progenitors. Three of the six intermediate clusters highly expressed ATP and oxidoreduction metabolic genes, and were marked as high-metabolic intermediates
