Extended Data Fig. 1: Second set: scRNA-seq of pulmonary melanoma identifies gene signatures in CD206hi IMs, CD206lo IMs and recMacs.
From: Chemokine-defined macrophage niches establish spatial organization of tumor immunity
(a) Unbiased UMAP clustering of scRNA-seq data from flow-sorted extravascular CD64⁺CD11b⁺ mononuclear phagocytes isolated from the lungs of WT C57BL/6 mice 16 days after intravenous injection of 4×105 B16F10 melanoma cells. Alveolar macrophages (AMs), interstitial macrophages (CD206hi IMs and CD206lo IMs); recruited macrophages (recMacs), classical and nonclassical monocytes, dendritic cells (DC1), DC2 (CD301+ and CD301−), migratory DCs (Mig DCs), neutrophils, T cells, B cells, fibroblasts, endothelial cells and cycling cells. (b) Top 3 DEGs defining the UMAP clusters as in a (c-h) Violin plots comparing gene expression in CD206hi IMs (dark blue) and CD206lo IMs (light blue) and recMacs (pink). (c) Violin plot shows the expression of C1qb as a key IM signature gene. Violin plots depict expression of (d) Mrc1, Pf4 Folr2, Cd163, and Mmp9 for CD206hi IM, (e) H2-Ab1, Tmem119, and Mmp12 for CD206lo IM, (f) Ccr2, Ly6c2, Vcan, and Thbs1 for recMacs, (g) Cxcl13, and Cxcl10 for IMs, and (h) Arg1, Vegfa and Cd274 by recMacs, and Trem2 for IMs and recMacs. (i) Dot plot shows the expression of curated genes in 16 immune cell populations (as in a). (j) Feature plot showing the expression of Ccl2 (as in a).
