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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. 10 — a, Label transfer uncertainty shown per cell type, comparing cells from control samples (‘healthy’, blue) to cells from IPF samples (orange). Results are shown per dataset, only showing datasets that include both control and IPF mapped samples. Alveolar fibroblasts, the cell type chosen for downstream analysis, are boxed in red. AT: alveolar type. DC: dendritic cell. TB: terminal bronchiole. EC: endothelial cell. Mph: macrophage. MT: metallothionein. NK: natural killer. SM: smooth muscle. b, Composition of alveolar fibroblast clusters by study. c, Expression of several genes highly expressed in IPF-enriched alveolar fibroblast cluster 0, shown per cluster. Cluster 0 is split into control (‘Healthy’) and IPF, further subdivided by study. d, Composition of monocyte-derived macrophage (MDM) clusters by study. e, As d, but by tissue sampling method. f, Expression of MDM cluster marker genes shown per cluster, with clusters split into studies. Studies with fewer than 200 were grouped into ‘Other’ for each cluster. g, Composition of MDM clusters by study, subsetted to only cells from donors with COVID-19. h, As g, but by tissue sampling method. i, As g, but subsetted to cells from donors with IPF. For c and f, mean expressions were normalized such that the highest mean expression was set to 1 for each gene. BALF: bronchoalveolar lavage fluid. IPF: idiopathic pulmonary fibrosis.