Extended Data Fig. 6: Extended information about immune populations identified by scRNA-seq in LLCAR+ and LLCAR lungs ± 20 Gy.
From: Radiation-induced amphiregulin drives tumour metastasis
a, Unsupervised uniform manifold approximation and projection (UMAP) of 32,690 live CD45+ cells in the lungs of LLCAR+ and LLCAR− tumour-bearing mice ± 20 Gy, n = 4 mice per group, annotated into 11 major cell lineages. Conv. type I DC = conventional type I dendritic cells, Alv. Mac = alveolar macrophages, Treg = regulatory T cells, NK cell = natural killer cells, ILC2 = group 2 innate lymphoid cells. b, UMAP of CD45+ cells stratified by condition; monocytes, B cells, T cells, NK cells, and neutrophils are outlined. c, t-SNE projection of the global transcriptomic profile from 16 individually hashtagged mice across four conditions. d, Bubble plot showing the top three marker differentially expressed genes (DEGs) for 11 major cell lineages. DEGs identified by two-sided Wilcoxon rank-sum test. e, Volcano plot of DEGs in monocytes from LLCAR+ + 20 Gy. Selected genes are coloured by function. P-values of 0 are depicted at 1−50 (log10). Two-sided Wilcoxon rank-sum test. f, Volcano plot of DEGs in monocytes from LLCAR− + 20 Gy. Selected genes are coloured by function. Two-sided Wilcoxon rank-sum test. g, UMAP of MNPs stratified by experimental condition. Monocytes, conv. type I DCs, plasmacytoid DCs, migratory DCs, and alveolar macrophages are outlined. Annotations assigned using Pegasus auto-annotation and top DEGs. Alv_mac = alveolar macrophage, cDC1 = conventional type 1 DC, pDC = plasmacytoid DC. Cluster colours consistent with Fig. 3c. h, Dot plot and bar graph showing the fraction of cells in 17 MNP subclusters across conditions. Mono = monocyte, Alv_macro = alveolar macrophage, Plasm_DC = plasmacytoid DC, Mo_DC = monocyte-derived DC, Int_macro = interstitial macrophage, Migr_DC = migratory DC, Class_DC_1 = classical type 1 DC. i, Volcano plot of DEGs in population 1 (Mono_Fn1). Selected genes are coloured by function. P-values of 0 are depicted at 1−50 (log10). Two-sided Wilcoxon rank-sum test.
