The expression of well-known MSN marker genes, including PP1R1B, BCL11B, and PDE1B,23,24 indicated which clusters contained MSNs (Figures S1E-S1G). Differential gene analysis of those MSN clusters vs. other clusters revealed several other MSN markers, including KIAA1211L, PDE2A, SLIT3, and NGEF (Figures S1H-S1K). To identify MSN subtypes, we recalculated the PCAs and performed dimensionality reduction on the isolated MSN nuclei, clustered them at a resolution that distinguished physically separated UMAP clusters, and annotated them using FISH probes against a mixture of previously described16,25,26 and novel marker genes (Data S1; Figures 2A-2C and 4-7). The clusters putatively corresponded to D1- and D2-MSNs in the matrix (D1M and D2M), D1- and D2-MSNs in striosome (D1S and D2S), D1- and D2-MSNs in the NAc shell and olfactory tubercle (OT) (D1Sh and D2Sh), and MSN-like neurons located in the interface islands (Figure 2A). One cluster was a D1/D2-hybrid (D1/2) and shared many characteristics with a novel MSN type described in rodents (D1H or eccentric-SPN).15,17 Each MSN cluster was signified by groups of differentially expressed genes that were specifically enriched in that cluster (Figures 2C and
