Extended Data Fig. 5: Cell-intrinsic programs and epithelial regenerative cell states in the COVID-19 lung cell atlas.
From: COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
a, b, Differences in cell composition across donors. Percentage of cells (y axis) from each myeloid subset (legend) in each donor (x axis). b, Percentage of cells (y axis) from each main lineage (legend) in each donor (x axis), rank ordered by proportion of epithelial cells (blue). c, Myeloid, endothelial and pneumocyte cells show substantial changes in cell intrinsic expression profiles in COVID-19 lung. log2(fold change) (y axis) between COVID-19 and healthy lung for each elevated gene (dot) in each cell subset (x axis, by automatic annotation). Black bars, number of genes with significantly increased expression (adjusted P < 7.5 × 10−6). Computed using a single cell-based differential expression model applied to a meta-differential expression analysis between COVID-19 and healthy samples across 14 studies (see Supplementary Methods). d, PATS and IBPLP cells in COVID-19 lung. UMAP embeddings of 1,550 KRT8+ PATS-expressing cells (top) or of 1,394 airway epithelial cells (bottom) coloured by IPBLP cells or basal cells (orange, leftmost panels) or characteristic markers (purple, remaining panels).
