For MSN analysis, we isolated the clusters that were enriched with well-known marker MSN genes including PP1R1B, BCL11B, and PDE1B. In order to balance the number of nuclei per animal, we randomly sampled MSN and MSN-like nuclei from monkey P to levels of monkey F (7,387 nuclei). We then re-calculated principal components (PCs) and performed UMAP dimensionality reduction on the first 15 PCs. We used Louvain clustering and chose a resolution that separated clusters that were distinct in UMAP space. We calculated the differentially expressed genes for each MSN subtype with the FindMarkers function (Data S1). To determine whether the clustering of MSNs was exhaustive, we further isolated ‘D1-’ and ‘D2-MSNs’. D1-MSNs including D1-striosome, D1-matrix and D1-shell/OT, whereas D2-MSNs included D2-striosome, D2-matrix and D2-shell/OT. We re-calculated PCs and performed UMAP dimensionality reduction based on the top 15 PCs for both subclusters. This analysis recovered the same, physically distinct clusters observed in the integrated analysis. To analyze the interneuron populations, we isolated clusters based on interneuron markers.18 Similarly, we re-calculated PCs and performed UMAP dimensionality reduction on the first 30 PCs.
