Extended Data Fig. 8 |. DATPs and lung regeneration.

a, Expression of selected, previously established cell-type-specific signatures (y-axis) in cell types defined in this study (x-axis). Dot size indicates fraction of cells and colour indicates expression level. b, c, Expression of selected genes (y-axis) in different cell types (x-axis), highlighting high expression of B2M in cycling epithelial cells (b) and collagen genes in ECM^high epithelial cells (c). d, Fraction of KI67⁺ cells among pro-SPC⁺ cells in structurally preserved versus damaged areas (n = 3 distinct areas each) from a COVID-19 lung. Mean ± s.d., t-test. e–g, UMAP embedding of alveolar epithelium and expression of selected genes that define the DATP signature. h, Composite expression of the three-gene DATP signature. i, Expression of the refined DATP signature (see Methods). j–n, First three DCs showing group assignment (j), cell or cell-state assignment (k), expression of AT2 signature (l), AT1 signature (m; log-normalized, see Methods), and effect of PMI (n). o, Gene set enrichment analysis in DATPs (compared to AT1 and AT2 cells). Rows indicate pathways in descending order of enrichment or significance (see key); x-axis indicates FDR. p, Inference of G2/M and S phase of individual DATPs (dots) (see Methods). q, Representative immunofluorescence staining (DATP marker CLDN4 and AT2 cell marker HTII-280) in control and COVID-19 lung tissue sections. Dashed boxes indicate areas highlighted to the right of each image. Scale bar, 50 μm. r, s, Quantification of KRT8⁺ (r) and CLDN4⁺ (s) cells in a subset of tissue sections from control and COVID-19 lungs. Mean ± s.d., t-test. q–s, Control, n = 3 donors; COVID-19, n = 4 donors. t, Coefficient of determination (R²) of days from symptom onset to death and AT2/AT1 ratio. Error bands, 95% standard error interval on the Pearson correlation (n = 18 donors).