Both D1- and D2-MSNs derived from the DS split into two clusters; one larger cluster and one smaller cluster. We reasoned that the larger D1- and D2-MSN clusters likely corresponded to the matrix (Figure 2A, dark and light blue clusters, respectively), whereas the smaller clusters likely corresponded to striosomes (Figure 2A, light and dark red clusters, respectively). The genes most enriched in the striosome MSNs (D1S and D2S) were KCNT1, KHDRBS3, FAM163A, BACH2, and KCNIP1, whereas the genes most enriched in the matrix MSNs (D1M and D2M) were EPHA4, GDA, STXBP6, and SEMA3E (Figures 2C and S4A) (p < 1.77 x 10−52 , Wilcoxon). KCNIP1 is the gene for the the potassium channel-related KChIP1, and staining for KChIP1 labels the boarders of the striosome (Figure 4I).32 We performed FISH labeling with KCNIP1 and STXBP6 – a highly specific matrix marker – and the results show a similar pattern as the KChIP1 antibody labelling (Figures 4J and 4K). Similar patterns were observed using FISH probes that labeled other identified striosome and matrix markers (Figures 4K and S4B-S4D). Thus, these results confirm
