Extended Data Fig. 8: Macrophage sub-populations.
From: Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy
a, Uniform manifold approximation and projection (UMAP) representation of 53,730 nuclei classified as macrophage or proliferating macrophage in the global analysis colored by sub-population. b, UMAP plot with the S phase cell cycle score overlaid (see Methods). c, UMAP plot with the G2M phase cell cycle score overlaid (see Methods). d, Expression of markers for each sub-population. The size of each dot reflects the percent of nuclei expressing the gene at non-zero levels and the shade reflects the mean log-normalized expression. e, Distribution of macrophage sub-populations across patients (nDCM = 11, nHCM = 15, nNF = 16) by disease status, with statistically credible differences denoted with a *, see Methods. Center line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; points, outliers. f, Representative immunofluorescence staining for macrophage marker CD163, cycling marker MKI67, and nuclei with DAPI from single tissue sections of four patients. The percent of macrophages with MKI67 expression across full tissue sections are shown on each image. g, Dendrogram demonstrating similarity of sub-population centroids based on the top 2000 most highly variable genes using Euclidean distance and the Ward method. h-i, Expression of marker genes for CCR2 positive (CCR2+) (h) and CCR2 negative (CCR2-) (i) cardiac macrophages obtained from Bajpai et al., 201815. The size of each square represents the percent of nuclei expressing the gene at non-zero levels while the shade represents a log fold-change (log(FC)) estimate comparing the expression in the given sub-population to all other sub-populations. Genes significantly up- or down-regulated in a sub-population (FDR < 0.01, as calculated with the Benjamini-Hochberg procedure) are shown with a black border. Mφ, Macrophage; NF, Non-failing; DCM, Dilated cardiomyopathy; HCM, Hypertrophic cardiomyopathy; Pct nuclei expr > 0; Avg norm expr, Average normalized expression scaled to the max expression for each gene across all sub-populations.
