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a, Heatmap showing smoothed RNA gene expression–based CNV patterns across meta-cells of pan-cancer cell lines. The karyotypically normal diploid cell line <t>IMR90</t> is highlighted. Hierarchical clustering of CNV patterns was performed within each cell line, and no statistically significant subclones were identified. b, PCA plot showing the distribution of cell lines along the first two principal components based on inferred gene-level CNV profiles. Cell lines with close genetic evolutionary proximity, as well as IMR90, are highlighted. c, Comparison of genome-wide CNV profiles inferred from scRNA-seq in this study with published WES-derived CNV profiles from Jacob et al. for 786-M1A, H2030-BrM3, MDA231-BrM2, and PC9. d, Comparison of chr20 amplifications in SK-BR-03 between published WGS-derived CNV data and scRNA-seq-based inferCNV from this study. e, Comparison of chr20 CNV profiles in HT-29 between published WGS-derived CNV data and scRNA-seq-based inferCNV from this study.
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a, Heatmap showing smoothed RNA gene expression–based CNV patterns across meta-cells of pan-cancer cell lines. The karyotypically normal diploid cell line <t>IMR90</t> is highlighted. Hierarchical clustering of CNV patterns was performed within each cell line, and no statistically significant subclones were identified. b, PCA plot showing the distribution of cell lines along the first two principal components based on inferred gene-level CNV profiles. Cell lines with close genetic evolutionary proximity, as well as IMR90, are highlighted. c, Comparison of genome-wide CNV profiles inferred from scRNA-seq in this study with published WES-derived CNV profiles from Jacob et al. for 786-M1A, H2030-BrM3, MDA231-BrM2, and PC9. d, Comparison of chr20 amplifications in SK-BR-03 between published WGS-derived CNV data and scRNA-seq-based inferCNV from this study. e, Comparison of chr20 CNV profiles in HT-29 between published WGS-derived CNV data and scRNA-seq-based inferCNV from this study.
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a, Heatmap showing smoothed RNA gene expression–based CNV patterns across meta-cells of pan-cancer cell lines. The karyotypically normal diploid cell line <t>IMR90</t> is highlighted. Hierarchical clustering of CNV patterns was performed within each cell line, and no statistically significant subclones were identified. b, PCA plot showing the distribution of cell lines along the first two principal components based on inferred gene-level CNV profiles. Cell lines with close genetic evolutionary proximity, as well as IMR90, are highlighted. c, Comparison of genome-wide CNV profiles inferred from scRNA-seq in this study with published WES-derived CNV profiles from Jacob et al. for 786-M1A, H2030-BrM3, MDA231-BrM2, and PC9. d, Comparison of chr20 amplifications in SK-BR-03 between published WGS-derived CNV data and scRNA-seq-based inferCNV from this study. e, Comparison of chr20 CNV profiles in HT-29 between published WGS-derived CNV data and scRNA-seq-based inferCNV from this study.
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a, Heatmap showing smoothed RNA gene expression–based CNV patterns across meta-cells of pan-cancer cell lines. The karyotypically normal diploid cell line <t>IMR90</t> is highlighted. Hierarchical clustering of CNV patterns was performed within each cell line, and no statistically significant subclones were identified. b, PCA plot showing the distribution of cell lines along the first two principal components based on inferred gene-level CNV profiles. Cell lines with close genetic evolutionary proximity, as well as IMR90, are highlighted. c, Comparison of genome-wide CNV profiles inferred from scRNA-seq in this study with published WES-derived CNV profiles from Jacob et al. for 786-M1A, H2030-BrM3, MDA231-BrM2, and PC9. d, Comparison of chr20 amplifications in SK-BR-03 between published WGS-derived CNV data and scRNA-seq-based inferCNV from this study. e, Comparison of chr20 CNV profiles in HT-29 between published WGS-derived CNV data and scRNA-seq-based inferCNV from this study.
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a, Heatmap showing smoothed RNA gene expression–based CNV patterns across meta-cells of pan-cancer cell lines. The karyotypically normal diploid cell line IMR90 is highlighted. Hierarchical clustering of CNV patterns was performed within each cell line, and no statistically significant subclones were identified. b, PCA plot showing the distribution of cell lines along the first two principal components based on inferred gene-level CNV profiles. Cell lines with close genetic evolutionary proximity, as well as IMR90, are highlighted. c, Comparison of genome-wide CNV profiles inferred from scRNA-seq in this study with published WES-derived CNV profiles from Jacob et al. for 786-M1A, H2030-BrM3, MDA231-BrM2, and PC9. d, Comparison of chr20 amplifications in SK-BR-03 between published WGS-derived CNV data and scRNA-seq-based inferCNV from this study. e, Comparison of chr20 CNV profiles in HT-29 between published WGS-derived CNV data and scRNA-seq-based inferCNV from this study.

Journal: bioRxiv

Article Title: Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features

doi: 10.64898/2026.05.31.729161

Figure Lengend Snippet: a, Heatmap showing smoothed RNA gene expression–based CNV patterns across meta-cells of pan-cancer cell lines. The karyotypically normal diploid cell line IMR90 is highlighted. Hierarchical clustering of CNV patterns was performed within each cell line, and no statistically significant subclones were identified. b, PCA plot showing the distribution of cell lines along the first two principal components based on inferred gene-level CNV profiles. Cell lines with close genetic evolutionary proximity, as well as IMR90, are highlighted. c, Comparison of genome-wide CNV profiles inferred from scRNA-seq in this study with published WES-derived CNV profiles from Jacob et al. for 786-M1A, H2030-BrM3, MDA231-BrM2, and PC9. d, Comparison of chr20 amplifications in SK-BR-03 between published WGS-derived CNV data and scRNA-seq-based inferCNV from this study. e, Comparison of chr20 CNV profiles in HT-29 between published WGS-derived CNV data and scRNA-seq-based inferCNV from this study.

Article Snippet: IMR90, MeWo, RPMI7951, Sk-Mel-24, Sk-Mel-3, DB, GA-10-Clone-4, MOLT-4, HL-60, U2-OS, and MP41 cell lines were obtained from the American Type Culture Collection.

Techniques: Gene Expression, Comparison, Genome Wide, Derivative Assay