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. 2023 Jun 8;29(6):1563–1577. doi: 10.1038/s41591-023-02327-2

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 4 — a, A UMAP embedding of all cells annotated as dendritic cells, colored by final detailed annotation (left), and by expression of three migratory DC marker genes (right, CCR7, LAD1, and CCL19). b, Expression of migratory DC marker genes from a among migratory DCs (red, right half of violins) versus other DCs (gray, left half of violins), split by study. Number of migratory DCs per study is specified in the x-axis labels. c, Expression of markers for two novel immune cell types (hematopoietic stem cells and migratory DCs, found in 9 and 10 out of 11 studies, respectively), shown per stromal cell type. d, Expression of markers for three novel epithelial cell types (hillock-like, AT0, and pre-TB secretory cells, found in 9, 9, and 11 out of 11 studies, respectively), shown per epithelial cell type. Two markers shared between AT0 and pre-TB secretory cells are also included. e, Expression of markers for a novel stromal cell type (‘smooth muscle FAM83D+’, found in 8 out of 11 studies), including three general smooth muscle marker genes and one marker gene uniquely expressed in FAM83D+ smooth muscle cells (FAM83D), shown per stromal cell type. For c-e, gene counts were normalized such that the maximum expression of a group of cells in the plot was set to 1. f, FAM83D expression across stromal cell types. Cells annotated as FAM83D+ smooth muscle are split by study. Studies with fewer than 3 smooth muscle FAM83D+ cells are not shown. DC: dendritic cell. Mph: macrophage. MT: metallothionein. AT: alveolar type. SMG: submucosal gland. TB: terminal bronchiole.