To characterize each cell, cells from organoids were clustered into 29 clusters according to their transcriptome features (Figure S3D-S3G). Notably, no significant difference in mapping ratio and total number of unique molecular identifiers (UMIs) were found among different clusters (Figure S4A). GO analysis and expression pattern of unique markers functionally annotated each cluster (Figure 5C). First, we isolated ten “neuronal” clusters by the high expression of general neuronal markers (STMN2, GAP43 and DCX) and the lack of early neurogenesis genes (VIM, NES and HES1) (Figure S3F and S3G). Interneurons, marked by GAD1 and the interneuron-specific neuropeptides TAC1, were significantly enriched in five neuronal clusters (IN1-5) from hMGEOs, while hCOs also generated interneurons (Fig. 5D and 5E). hMGEOs rarely produced cortex-specific cell types (CN1-2). TBR1+ and NEUROD2+ cortical neurons were mainly from hCOs (Figure 5D). Comparative analysis of hMGEOs- and hCOs-derived interneurons revealed that NKX2-1 expression was negligible in hCOs-derived interneurons (Figure 5F). Some neurodevelopmental genes (e.g. MAP2 and ALCAM) were enriched in hMGEOs-derived interneurons, whereas hCOs-derived interneurons displayed higher cortical developmental genes (e.g. ZIC1, PTN and MEIS2) (Inoue et al.,
