Extended Data Fig. 4: Cell-type annotation for the immune lineage using UMAP plots and spatial data.

a, Lineage-level UMAP for immune cells generated after final cell-type annotation. b, Select cell-type gene markers visualized in UMAP space across immune cells. c,e, UMAPs were additionally visualized for lymphoid (c) and myeloid cell types (e) separately. d,f, Specific gene markers for lymphoid (d) and myeloid cell types (f) visualized in UMAP space. For b, d and f, the specific cell types or groups of cells marked by each gene are listed near the gene name. g,h, Individual examples of Langerhans cells (g) and neutrophils (h) indicated by white arrows with individual transcripts overlain onto H&E tissue stains. g, Langerhans cells in sample TILD117MA1 (IPF diagnosis) expressing immune marker PTPRC, dendritic cell markers CD1C and HLA-DQA1, and specific Langerhans cell markers CD1A and FCGBP in a remodeled airspace marked by SFTPC. h, Neutrophils in unaffected sample VUHD116B expressing general myeloid/monocytic markers FCGR3A, S100A8, S100A9 and S100A12 in addition to specific neutrophil marker SLC25A37. See Extended Data Fig. 1 for a dotplot heatmap showing expression of marker genes in each cell type.