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. 2022 Nov 9;611(7936):594–602. doi: 10.1038/s41586-022-05425-2

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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. 9 — a, P2-LN1 sample (left) DAPI image with BaSISS subclone fields (as shown in Fig. 5a) and coloured squares mark regions depicted in b,c,d; (middle) pan-cytokeratin immunohistochemistry stained (IHC) (epithelial cells appear brown); (right) CD45 antibody (immune cells appear brown) with ISS immune panel derived cell types projected as coloured dots. b—d, Snapshots of example regions dominated by P2-blue or P2-orange clones, as indicated in a. In each case signals (dots) from selected targets in BaSISS b, ISS oncology c or ISS immune panels d are presented overlaid on sections stained by IHC following the BaSISS/ISS experiment. In the bottom row of c and top row of d inferred epithelial and immune cell types are presented. In top rows of c and d, 80% transparency is applied to the underlying IHC image to aid visualisation of overlaid dots. e, Spatial patterns of three hypoxia related genes are projected on the entire P2-LN1 tissue section. f, Spatial patterns of PDGFRB, CD34, CD68 and hypoxia related ISS signals overlaid on HER2 (left) and CD45 IHC stained sections(right) correspond to region of white square on top left clone field image in e.