optical clearing (Fig. 2e). Interestingly, we also observed processes of Dlxi1/2b::eGFP+ cells that briefly touched VZ-like regions, reminiscent of rodent ventricle-directed migration18 (Supplementary Video 3; Extended Data Fig. 5m–o). We next investigated the fate of Dlxi1/2b::eGFP+ cells in hSS after 2 weeks of migration from hSS into hCS by isolating single cells and performing transcriptome analysis (Extended Data Fig. 6a). We found that the majority of migrated cells expressed subpallial markers (DLX1, DLX2, DLX5, DLX6) and cortical interneuron markers (GAD1, GAD2, VGAT, CELF4) (Extended Data Fig. 6b; Extended Data Fig. 7a–d). We found few cells expressing PAX6 or TH, which are indicative of olfactory interneurons, or SP8, GSX2 or CHAT, which are indicative of striatal neurons, suggesting that the Dlxi1/2b reporter is primarily labelling cortical interneurons (Extended Data Fig. 6b).
