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. 2022 Dec 21;55(1):66–77. doi: 10.1038/s41588-022-01243-4

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© The Author(s) 2022

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. 1 — (a) H&E sections of full depth human tissue samples from multiple regions showing all major structures of the lungs and airways. (b) Expression of cell type marker genes in the master cell type groups, from both single cell and single nuclei RNA-seq combined. Color represents maximum normalised mean expression of marker genes in each cell group, and size indicates the proportion of cells expressing marker gene. Dashed box highlights chondrocyte marker genes. (c) Variance of gene expression explained by metadata variables in the combined sc/snRNA-seq dataset, scRNA-seq and snRNA-seq datasets. The whiskers correspond to 95% confidence intervals and the number of genes tested was 8,666 in cells/nuclei combined, 7,977 in cells, 7,260 in nuclei. 129,340 cells and 63,768 nuclei were analysed. (d) Protein staining of chondrocyte markers in the cartilage of human bronchus from the HPA. (e) Proportion of mesenchyme cell type groups in the airways from cells and nuclei. Numbers indicate chondrocytes in single cells versus single nuclei. (f) UMAP of sequencing material (cells or nuclei) and location (trachea, bronchi, parenchyma).