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. Author manuscript; available in PMC: 2021 Apr 26.
Published in final edited form as: Nat Genet. 2020 Oct 26;52(11):1158–1168. doi: 10.1038/s41588-020-00721-x

Extended Data Fig. 4. Sub-clustering of cells from the substantia nigra identifies TH-positive dopaminergic neurons.

Extended Data Fig. 4

a-d, UMAP dimensionality reduction after iterative LSI of scATAC-seq data from substantia nigra cells from 2 different samples. Each dot represents a single cell (N = 11,199). Dots are colored by (a) their corresponding substantia nigra sub-cluster, (b) the sample of origin, or (c-d) its gene activity score for (c) the tyrosine hydoxylase (TH) gene, a specific marker of dopaminergic neurons or (d) other lineage-defining genes. In (c-d), gene activity scores were imputed using MAGIC. Grey represents the minimum gene activity score while purple represents the maximum gene activity score for the TH gene. In (a-c), the minimum and maximum scores are shown in the bottom left of the figure. Predicted cluster cell type identities are overlaid on the UMAPs.