We annotated our cells from the human or monkey striatum to a recently published high-resolution snRNA-seq reference dataset of the non-human primate striatum34 using Seurat v4. We downloaded the monkey snRNA-seq processed, annotated gene UMI counts for all cells and MSNs from GSE167920. He, Kleyman et al. had aligned the snRNA-seq reads to the rheMac10 genome using the GRCh38 gene annotation liftover to rheMac10, so the gene-wise labels represent the UMI counts on the rheMac10 genome most orthologous to human. For both full nuclei and MSN subset datasets, we re-processed the macaque cells with SCTransform, glmGamPoi, and reciprocal PCA with default parameters as above to enable label transfer using the most recent integration algorithms in Seurat.
