To compare in vitro-derived neurons to those generated in vivo, we analyzed the gene expression of cells derived from four human fetal neocortical samples at approximately 100 days post-conception (dpc). FACS was used to sort fixed cortical progenitors (SOX2hi) and neurons (SOXlo/−PAX6+) for gene expression profiling (Thomsen et al., 2016). 100-cell pools from seven reproducibly-observed populations were evaluated by RNAseq (Figure 2C). Populations expressing high levels of SOX2 were composed of neuronal and glial precursors, including a mixture of radial glia and intermediate precursors (P4: EOMES, PAX6, HOPX, VIM), astrocyte precursors (P11: AQP4), and oligodendrocyte precursors (P10: OLIG1, PDGFRα) (Figure 2D). Fetal projection neurons were SOX2− P6-P7. Only two populations expressed detectable levels of GAD1: P8 and P9. The P8 population likely consists of LGE-derived interneurons, express expressed PAX6 and SP8. The P9 population expressed the highest levels of GAD1, and was the only population to show substantial expression of SST or LHX6, indicating this population is enriched for cortical interneurons. We performed principal component analysis (PCA) with the top 1% of genes based on maximum pairwise fold change across
