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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. 10 — (a) Expression dot plot of genes relevant for Figure 5h. (b) Co-staining of CCL28 RNA/protein and IgA2 protein in airway submucosal glands, left: smFISH; right: IHC for CCL28. (c) Expression of TNFSF13, IL-6 and CCL28 in SMG-Serous and Duct cell sc/snRNAseq data along the tracheobronchial tree. Change in CCL28 in serous cells was statistically significant with two-sided Spearman’s rank correlation (methods) (p-values 1.6 × 10-8, 0.0034 and 1.3 × 10-5 for donors A37, A41 and A42 correspondingly). (d) smFISH on the human trachea with DAPI, TNFSF13/APRIL, RARRES1 and LPO. Dashed lines show regions of duct, mucous and serous glands. (e) smFISH (TNFSF13/APRIL, and CD79A) and IHC (IgA2) of human tracheal SMG showing APRIL+ and APRIL- glands annotated. (f) Violin plot for expression of AICDA in B cell subsets. (g) IHC from the HPA showing HLA-DR, MUC5B and PRR4 staining with HLA-DR+ regions corresponding with non-mucous areas of gland. Red/purple dashed lines indicate mucous/serous cells respectively based on morphology and/or marker gene expression. (h) smFISH (MUC5B) plus IHC (HLA-DR) staining in human airway SMG. (i) IHC staining of CD4, CD45RO (memory marker), CD45RA (naive marker), IgA2 and EpCAM in the SMG. Blue arrows indicate CD4+CD45RA+ cells. (j) IHC staining of HLA-DR, EpCAM, CD3, CD31 and CD4 in the airway SMG. Arrows point to CD3+CD4+ cells. (k) IHC staining of CD4, CD45RO, HLA-DR and EpCAM in the airway SMG showing close interactions between CD4+CD45RO+ T cells with HLA-DR+ glands. Arrows point to CD4+CD45RO+ cells.