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. 2023 Apr 25;14:2383. doi: 10.1038/s41467-023-38034-2

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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 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. 8 — a–e Single-cell RNA-seq analyses of osteosarcoma-like lesions. a Diagram for LIGER data integration of single-cell RNA-seq datasets of lineage-traced tdTomato⁺ cells isolated from Fgfr3-creER; Trp53^fl/+; R26R^tdTomato (Fgfr3-p53 cHet) and Fgfr3-creER; Trp53^fl/fl; R26R^tdTomato (Fgfr3-p53 cKO) femurs at 4M (pulsed at P21). Fgfr3-p53 cHet: 1696 cells, Fgfr3-p53 cKO: 2015 cells, Total: 3711 cells. b UMAP visualization of major sub-clusters of the LIGER-integrated dataset. c UMAP visualization of two datasets integrated by LIGER. Blue: cHet, red: cKO. d Density plots of Fgfr3-p53 cHet (left) and Fgfr3-p53 cKO (right) in the integrated space. Red dotted contour: OCT Stem and Chondrocyte-like clusters predominantly contributed by Fgfr3-p53 cKO cells. e Split violin plots for Mki67 (proliferation), Acan (Chondro), Col1a1 (Osteo), and Cxcl12 (Reticular) in representative clusters (OCT Stem, Chondrocyte 1, Osteoblast 1, and Reticular 1) between cHet (blue) and cKO (red). n = 148 (OCT Stem), n = 26 (Chondro 1), n = 290 (Osteo 1), n = 469 (Reticular 1) cells in cHet. n = 426 (OCT Stem), n = 125 (Chondro 1), n = 177 (Osteo 1), n = 434 (Reticular 1) cells in cKO. f UMAP-based visualization of putative aneuploid cells inferred by CopyKAT. Blue: putative normal cells. Red: putative tumor cells. g Genome-wide visualization of copy number variations in putative tumor cells inferred by CopyKAT. h Hierarchical clustering of putative tumor cells with different patterns of copy number variation inferred by inferCNV. i REVIGO plot of gene ontology terms enriched among genes upregulated in putative tumor cells. The p values were calculated using GOrilla’s one-sided test based on the hypergeometric distribution, with a flexible p value cutoff applied for multiple testing correction. The results were subsequently transferred to REVIGO for visualization. j Mouse-human tumor data integration. Left: Diagram for LIGER data integration of single-cell RNA-seq datasets from mouse and human osteosarcoma cells. Center to the right: Fgfr3-p53 cKO scRNA-seq dataset was integrated with the human chondroblastic osteosarcoma scRNA-seq dataset (BC17). UMAP visualization of human chondroblastic and osteoblastic osteosarcoma cells in the integrated space (center left). Density plots of human (BC17) (center right) and mouse (right) tumor cells in the integrated UMAP space.