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. 2023 Aug 2;620(7973):409–416. doi: 10.1038/s41586-023-06367-z

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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 licence, and indicate if changes were made. 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/4.0/.

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Extended Data Fig. 4 — a, UMAP plot with the 2 integrated samples of patient 01-040 showing the normalized expression of major cell type markers: immune cells (PTPRC, also known as CD45), endothelial cells (PECAM), tumor cells (EPCAM, PGR, TFF3), CAF cells (ACTA2). b, Table showing the cell number in each cell type. c, Identification of CAFs subtypes (markers used: mCAFs: MMP2, DCN, COL12A1, FBLN1; vCAFs : MCAM, COL4A1, COL18A1; iCAFs.1: MUSTN1, TAGLN, S100A4, CXCL2; iCAFs.2: S100A8, CXCL8, SPLI). d, CAFs subcluster composition analysis, the left panel shows the total CAFs numbers per cluster in each condition and the right panel shows the proportion of CAFs per cluster in each samples. e, UMAP plot of sub-clustered CAFs showing other CAFs subtypes (markers used: myCAFs: ACTA2, CTGF, POSTN, PDGFR, TGFB1, COL1; iCAFs : IL6, CXCL1, CCL2, PDGFRA, HAS1, FAP, IL11, LIF; apCAFs: H2-AB1, CD74, SAA3). f, Violin plot showing CAFs subtypes scores before and after treatment (C1D1 or C3D1) (Wilcoxon test, two-sided).