The 1,307,323 cells were divided into 49 clusters using the FindNeighbors and FindClusters functions in Seurat. Cell clusters were annotated into known striatal cell types based on expression levels of a combination of marker genes curated from established studies (Fig. 2b)30,31,33,56,80. Cells were mapped to the Allen Institute Mammalian Basal Ganglia Consensus Cell Type Atlas34 for validation using the cell_type_mapper Python package provided by the Allen Institute.
