To investigate the cell-type-specific architecture of the NHP striatum, we micro-dissected the caudate nucleus (Cd), putamen (Pt), and ventral striatum (VS) from coronal sections of two monkeys (Figures 1A and S1A), performed snRNA-Seq, and clustered the nuclei profiles based on their gene expression counts (STAR Methods). Each major cluster had nuclei derived from both subjects (Figure 1B) and all regions (Figure 1C), indicating broad similarities between the subjects and the regions. Feature plots showed the expression of well-known marker genes and thus indicated the correspondence between nuclei clusters and broad cell classes including D1-MSNs, D2-MSN, striatal interneurons, and non-neuronal cell types (Figures 1D, S1C and S2). Each major cell class was signified by groups of differentially expressed genes that were specifically enriched in that cluster (Figures 1E and 1F; Data S1). The intersection of differentially expressed genes from each cluster with orthologous marker gene lists from several databases13,17,22 confirmed the identity of the clusters (p < 0.05, Benjamini-Hochberg corrected, Hypergeometric tests). Violin plots showing the expression levels of marker genes in each major class confirmed the basic validity of our
