Extended Data Fig. 7: Case-control scRNA-seq integrative analysis of SNpc. | Nature Neuroscience

Extended Data Fig. 7: Case-control scRNA-seq integrative analysis of SNpc.

From: Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson’s disease

Extended Data Fig. 7

a,b, Box plots showing, per individual, the median number of UMIs (A) and genes (B) per profile (n = 8 neurotypical controls and 10 PD/LBD samples). ns, not significant Wilcoxon rank-sum two-sided test p > 0.05. Center bar indicates median value and lower and upper hinges correspond to first and third quartiles respectively. Whisker distance from upper and lower hinges represent no more than 1.5*interquartile range. c,d, Violin plots of number of UMIs (C) and genes (D) per profile across eight major cell classes grouped by disease (PD/LBD, blue) and control (Ctrl, red). e-f, Box plots showing, per individual, the age at death (E) and postmortem interval (F) stratified by case (PD/LBD) and control (Ctrl) (n = 8 neurotypical controls and 10 PD/LBD samples). Center bar indicates median value and lower and upper hinges correspond to first and third quartiles respectively. Whisker distance from upper and lower hinges represent no more than 1.5*interquartile range (ns = not significant, Welch two sample t-test, p = 0.61 for (E) and p = 0.18 for (F). g, Stacked bar plot of sex stratified by disease status. h, Histogram of the year of collection of postmortem midbrain samples colored by case-control status (see Supplementary Tables 1 and 2 for raw values). i, Scatter plot of the collection year for each sample (x-axis) and the median number of UMIs (y-axis). Blue line indicates line of best fit as determined by lm.fit in R. Grey shading indicates standard error of fit. P-value corresponds to significance of slope from a mixed-effect model (see Methods). j–o, UMAP representations of Non-DA neurons (n = 91,479 nuclei) (J), Astrocytes (n = 33,506 nuclei) (K), Oligodendrocyte precursor cells (OPCs) (n = 13,691 nuclei) (L), Oligodendrocytes (n = 178,815 nuclei) (M), Endothelial cells/pericytes (n = 14,903 nuclei) (N), and Microglia/macrophages (n = 33,041 nuclei) (O) colored by cell type (left) and individual (right). P, Alignment scores (see Methods) for each of the seven non-DA cell classes.

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