Fig. 1: Spatial multi-omics atlas of the human lung allows the identification of cell types and their location.

a, Multi-omics spatial lung atlas experimental design included fresh and frozen sampling from five locations for scRNA-seq (seven donors), sc VDJ-seq (four donors), snRNA-seq (seven donors) and Visium ST (seven donors). Five donors (D) from the frozen samples were pooled into five reactions, each containing different locations (Loc) from donors. b, UMAP of all scRNA-seq/snRNA-seq from 193,108 cells/nuclei in total from ten donors. Cells from all major subsets were captured. c, cell2location mapping on Visium ST from a bronchi section shows matching of cell types to expected structures. H&E staining and cell abundance estimated by cell2location (density score) for ciliated, basal epithelium, AT1, AT2 and chondrocyte cell types with histology image in the background. Dotted lines circle the epithelium (pink), parenchyma (green) and cartilage (brown). d, Cell type groups are enriched in expected micro-anatomical tissue environments on Visium ST across sections from five donors. Cell type loadings are represented by both dot size and color for cell types annotated in b across the manually annotated micro-environments in the Visium data. e, Cell type capture is affected by protocol and location. Cell type proportion analysis with fold changes and LTSR score for all cell type groups with regard to the material, protocol and location. Dashed boxes highlight the greatest changes. AT1, alveolar type 1; AT2, alveolar type 2; LE, lymphatic endothelium; VE, vascular endothelium. The number of cells in each cell type group is shown in Supplementary Table 7 and online: https://www.lungcellatlas.org as variable Celltypes_master_high.