Extended Data Fig. 5: BAL Cell-Type Deconvolution and Imputed Cell-Specific Gene Expression.

Cell type fractions were imputed using bulk gene expression and a reference single cell lung atlas. (a) Mean centered, scaled fractions are depicted for each cluster and varied across clusters for Monocyte/macrophages, neutrophils, CD4 + T-cells, and CD8+ Tcells (Kruskal-Wallis p = 4.14 × 10-24, 3.81×10-5, 1.89×10-22, and 3.36×10-13, respectively). (b) Raw values are shown for specific cell types. (c) Monocyte/macrophage-specific expression of the ‘GOBP Myeloid Leukocyte Activation’ gene set was imputed. Genes that were statistically significantly differentially expressed across clusters were selected for the heatmap, and average cell-type specific gene expression across the 4 clusters is displayed. (d) Lymphocyte-specific expression of ‘GOBP Lymphocyte Activation’ gene set was imputed. Genes that were statistically significantly differentially expressed across clusters were selected for the heatmap, and average cell-type specific gene expression across the 4 clusters is displayed. n = 127, 74, 45, and 32 for Clusters 1-4, respectively. For all box-whisker plots: boxes indicate the median and interquartile range and whiskers extend to the largest value above the 75th percentile (or smallest value below the 25th percentile) that is within 1.5 times the IQR.