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. 2021 Jul 9;13:111. doi: 10.1186/s13073-021-00922-x

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© The Author(s) 2021

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. 1 — ScRNA-seq-based tumour microenvironment analysis of 18,403 single cells from 7 treatment-naive HGSTOC patients. A Schematic overview of the sampling site (ovary, omentum or peritoneum) and tissue type (normal or tumour tissue) of the 12 biopsies from seven treatment-naive patients as well as the analysis workflow. B t-SNE representation of all single cells colour-coded for their assigned major cell type (left) and for the expression of three marker genes used for this annotation as indicated on the top row. Marker genes: B cell (CD79A, IGHG3, IGKC), dendritic cells (CD1C, CD1A, CLEC9A), endothelial cells (CLDN5, PECAM1, VWF), fibroblasts (COL1A1, COL1A2, BGN), myeloid cells (CD68, LYZ, AIF1), ovarian stroma cells (STAR, FOXL2, DLK1), T cells (CD3D, CD3E, TRAG), epithelial cancer cells (EPCAM, PAX8, CD24). Dendritic cells remained co-clustered with myeloid cells in the first clustering step, but separated from myeloid cells before further subclustering based on established marker genes (CLEC9A, CD1C, CD1A). C Barplot showing for each of the 32 stromal and 11 cancer subclusters (from left to right) the number of cells, tissue type (normal or tumour), their distribution across the 7 patients, their distribution across sampling sites (ovary, omentum and peritoneum) and their correlation to the copy number alteration (CNA) profile of patient 1 using low-coverage whole-genome sequencing. D t-SNE visualisation of dendritic cell (up) and myeloid cells (down) subclusters containing tissue-specific cells enriched in the omentum, defined as Langerhans-like dendritic cells (DC_CD207) and lipid-associated macrophages (M_MMP9). E CNA profiles of fibroblasts compared to those from the tumour subclusters and monocyte subclusters using inferCNV confirming the CN stable profile of all fibroblast subclusters