Analysis of differentially-expressed genes revealed that transcription factors specifying MGE (e.g. NKX2-1, NKX6-2, DLX1, OLIG1, and FOXA2) were uniquely expressed in hMGEOs (Figure 4B and 4C). GABA synthesis enzymes, GAD1 and GAD2, were highly expressed in hMGEOs, and were also expressed in hCOs at late time point, indicating hCOs also produced GABAergic neurons without exogenous ventral patterning cues. Glutamatergic neuron markers GLUD1, vGLUT1, and vGLUT2 were highly enriched in hCOs. PAX6, NEUROG2, TBR1 and CTIP2, which regulate cortical neuron differentiation, were also enriched in hCOs. In addition, multiple genes involved in early neurogenesis (e.g. NES and NEUROG1) were commonly upregulated in hMGEOs and hCOs. Comparison with transcriptomes of multiple human fetal brain regions (Miller et al., 2014) revealed that hMGEOs and hCOs are most close to MGE and cortical domains (occipital neocortex, OCX and orbital frontal cortex, OFC) respectively (FDR<0.001) (Figure 4D). Overall, these results demonstrate hMGEOs and hCOs molecularly resemble the developing human MGE and cortex.
