Fig. 1

Integrative analysis of > 300,000 single-cell profiles from five inflammatory disease tissues and COVID-19 BALF. a Overall study design and single-cell analysis, including the integrative pipeline, a single-cell reference dataset, fine-grained analysis to identify shared macrophage states, and disease association analysis. b Number of cells and donor samples from each healthy and disease tissue. c Percent of variance explained in the gene expression data by pre-defined broad cell type, tissue, sample, and technology for the first and second principal component (PC1 and PC2) before and after batch effect correction. d iLISI score before and after batch correction to measure the mixing levels of donor samples and tissue sources. An iLISI (integration LISI) score of 1.0 denotes no mixing while higher scores indicate better mixing of batches. e Integrative clustering of 307,084 cells reveals common immune cell types from different tissue sources. f Immune cells from separate tissue sources in the same UMAP coordinates. Cells from the same cell types are projected next to each other in the integrative UMAP space. g Heatmap of cell-type lineage marker genes. Gene signatures were selected based on AUC > 0.6 and P < 0.05 by Bonferroni correction comparing cells from one cell type to the others