Fig. 3

Single-cell RNA-seq of total bronchoalveolar lavage fluid immune (BAI) cells population. a t-SNE plots showing detected lineages and sub-populations in BAI cells across conditions (e.g. Control means the cells derived from healthy donors). b t-SNE plot of aggregate BAI cells with identified sub-populations. c Cell population percentages across conditions determined to be significantly modulated according to Differential proportion Analysis (DPA). *p < 0.05, **p < 0.01 (Fisher’s exact test). Abbreviation: C, M, S indicate Control, Moderate, and Severe, respectively; Mac, Macrophage; Mons /DC, Monocytes/Dendritic cells; PMC, Plasma cells; EPC, Epithelial cells; NK, natural kill cells. d Expression of select marker genes across BAI cells as visualized on t-SNE plots. e Left: bubble plot showing representative GO terms according to cell types. Right: heatmap characterizing the expression signatures of top 50 specifically expressed genes in each cell type; the value for each gene is row-scaled Z score