Fig. 2: Single-nucleus RNA sequencing reports differences in gene expression patterns of PD lineages and identifies a PD T cell signature.

a Uniform manifold approximation and projection (UMAP) graphs showing nuclei from the substantia nigra color-coded by cell type/lineage. b Same as a but color-coded by condition. c Dot plot of select gene (x-axis) marker expression in major lineages in the substantia nigra (y-axis). Size indicates percentage expression, and color indicates normalized expression levels. d Same as a but for the cingulate cortex. e Same as b but for the cingulate cortex. f same as c but for the cingulate cortex. g Comparison between the differentially expressed genes (DEGs) in PD vs. control dopaminergic neurons in our dataset and those in Kamath et al. ⁷. The scatterplot shows DEGs with the Kamath et al. reported -log10 adjusted p-value on the x-axis and our -log10 adjusted p-value on the y-axis. The color of each DEG indicates if it is significant in both datasets vs only in Kamath et al. All of the DEGs we discovered were reported in Kamath et al. P values are two-sided. h Violin plot showing the gene expression of TH in control (orange) and PD (blue) in dopaminergic neurons (logFC PD vs. control: −0.374, two-sided p-value 1.66e-7, as determined via differential gene analysis). i Heatmap showing the scores of single cell hierarchical Poisson factorization (scHPF) gene factors (columns) projected on lineages (rows). j Heatmap showing the gene loadings for select cell select genes in each of the single-cell Hierarchical Poisson Factorization (scHPF) factors.