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. 2024 Oct 4;25(11):2097–2109. doi: 10.1038/s41590-024-01975-x

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, 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 licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

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Extended Data Fig. 4 — a. Heatmap of subject scores for Spectra programs within each cell type for each of 24 patients with RPRA and 6 healthy control subjects. Each column represents a single patient or subject. Rows are min-max scaled and are hierarchically clustered. Labels refer to clusters identified from the single-cell RNA-seq object in Fig. 3a. Tissue-resident alveolar macrophages (TRAM) clusters 1-7, proliferating macrophages (Prolif. MP), monocyte-derived alveolar macrophages (MoAM) clusters 1-4, perivascular macrophages (Periv. MP), monocytes (Mo) cluster 1-2, CD4 T cells (CD4 T) clusters 1,2, CD8 T cells (CD8 T) clusters 1-3, regulatory T cells (Treg), gd T cells and NK cells (gd T, NK), proliferating T cells (Prolif. T), type I conventional dendritic cells (DC1), type II conventional dendritic cells (DC2), migratory dendritic cells (Migr. DC), plasmacytoid dendritic cells (pDC), Mast cells (Mast), plasma cells (Plas.). b. Upset plot showing downregulated differentially expressed genes (DEGs) shared between TRAM subsets. c. Upset plot showing upregulated DEGs shared between TRAM subsets.