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. We used Louvain clustering and annotated the resulting clusters based on known interneuron markers. To explore the functional roles of these cell types, gene enrichment analysis was run using gprofiler80 with the following GO databases: Biological Process, Molecular Pathway, KEGG, and Human Phenotype ontology (Data S4). We calculated the cosine similarity for nuclei within and between clusters based on PCA space. We used a permutation test on the cosine similarity between pairs of clusters. We randomly shuffled the nuclei to mask the nuclei identity and recalculated cosine similarity. We repeated these 10,001 times and used within group and between group variance ratio to determine a P value. To compare the cell types between monkey and mouse MSNs, we first generated an orthologous gene list between mouse and rhesus macaque from BioMart Ensemble with one-to-one orthologous genes78,79 used for downstream analysis. We integrated our MSNs and MSN-like nuclei from the two monkeys with MSN types in Stanley et. al.15 based on
