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. 2020 Dec 8;6:90. doi: 10.1038/s41421-020-00214-5

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© The Author(s) 2020

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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Fig. 2 — a t-SNE projection of eight subsets of myeloid cells (each dot corresponds to one single cell) shown in different colors. b t-SNE plots of different myeloid cell clusters origin. c Expression of marker genes for each cluster illustrated in the t-SNE plots. d Heatmap of the differences in pathway activities scored per cell by GSVA analysis. e Representative mIHC images to show the distribution of CD68⁺CD206⁺CCL18⁺ macrophages: CD68 (yellow), CD206 (green), CCL18 (red), and DAPI (bule). White arrows (CD68⁺CD206⁺CCL18⁺), blue arrow (CD68⁺CD206⁺CCL18⁻). Scale bar, 50 μm. f Kaplan–Meier curve showing poor survival in patients with high proportion of CD68⁺CD206⁺CCL18⁺ macrophage vs low proportion (log-rank test, P = 0.001) in our cohort. g Kaplan–Meier curves of survival for the TCGA HCC patients grouped by the average expression (high versus low) of DC_c1_CLEC9A cell marker genes as annotated in Table S3. (log-rank test, P = 0.0036). h Volcano plot showing differentially expressed genes in DC_c1_CLEC9A cells between peri-tumor and tumor. Each red dot denotes an individual gene passing our P value and fold change thresholds.