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. 2020 May 27;12:47. doi: 10.1186/s13073-020-00741-6

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© The Author(s) 2020

Open AccessThis 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 5 — Parallel analysis of the tumor microenvironment in BC159-T#3. a tSNE plot of non-tumor cells (dots) from BC159-T#3 sample, color-coded by cluster; fibroblasts are circled. b tSNE plot of human fibroblasts (dots), color-coded by cluster (top panel). Heatmaps of single cells (bottom left panel) and averaged single cells (bottom right panel) represent the mRNA expression levels of well-known markers for fibroblasts. c Violin plots of MDK and IGFBP7 mRNA expression levels in three fibroblast clusters. Abbreviations: MyoCAFs, cancer-associated myofibroblasts; COL13A1 MatrixCAFs, COL13A1 expressing cancer-associated matrix fibroblasts; COL14A1 MatrixCAFs, COL14A1 expressing cancer-associated matrix fibroblasts. ****P < 0.0001, ***P < 0.001, **P < 0.01, *P < 0.05. d Validation of protein expression of IGFBP7 and MDK in fibroblasts (ACTA2 positive) from BC159-T#3 by immunohistochemistry staining. Scale bar, 100 μm. e tSNE plot of human macrophages (dots), color-coded by cluster (top panel). Heatmaps of single cells (bottom left panel) and averaged single cells (bottom right panel) represent the mRNA expression levels of well-known markers for macrophage subtypes. Abbreviation: LC-like cells, Langerhans cell-like cells. f tSNE plot of human T cells (dots), color-coded by cluster (top panel). Heatmaps of single cells (bottom left panel) and averaged single cells (bottom right panel) represent the mRNA expression levels of well-known markers of T cell subtypes