Fig. 3: FlowSOM analysis on immune cells in syngeneic mouse tumors.

a Concatenated FlowSOM plot of different syngeneic tumor mouse models showing various populations defined based on expression analysis. Major markers used for defining clusters are activated microglia (CD45 low CD11b low CX3CR1+ MHCII+), resting microglia (CD45 low CD11b low CX3CR1+ MHCII−), monocytes (CD11b+ F4/80− CD64+ CX3CR1+ CD11c−), resident macrophages (CD11b+ F4/80+ CD64+ Ly6C−), Ly6G+ myeloid cells (Ly6G+ Ly6C+ CD11b+), infiltrating macrophages (CD11b+ F4/80+ CD64+ Ly6C+), Type B DCs (CD11c++ CD11b+ MHCII+), Type A DCs (CD11c++ CD11b+ MHCII−), CD103+ DCs (CD103+ CD11c+), classical CD4 (CD3+ CD4+ CD44+ MHCII+ Tim3− Lag3− CD25−), exhausted CD4 (CD3+ CD4+ Tim3+ Lag3+), CD4 T regs (CD4+ CD25+ KLRG1+ CD103+), exhausted CD8 (CD39+ Tim3+ Lag3+ CD8+), IgM+ B cells (B220+ IgM+), TCRgd T cells (TCRgd+ CD3+), NKT cells, (NK1.1+ CD49b+ CD3+ CD8+), NK cells (NK1.1+ CD49b+ CD3−), SiglecF+ Macrophages (SiglecF+ CD11b+ MHCII+ F4/80+), eosinophils (SiglecF+ CD11b+ MHCII−), classical CD8 (CD3+ CD8+ CD44+ MHCII+ Tim3− Lag3− CD25−), tumor-reactive CD8 (CD39+ CD103+ CD8+). b–d Abundance analysis on microglial clusters, innate immune cells, and adaptive immune cells in four tumor types as defined in a. Data represented as average ± SE for n = 3 mice/group; Representative data from two independent experiments. e Tumors were classified into immunologically active (GL261 and 005) and immunologically silent (CT2A and Mut3) based on RNAseq analysis. FlowSOM analysis was performed followed by abundance analysis. Populations that were significantly different were plotted. Data is represented as average ± SE for each cluster characterized. Two-sided Student’s t test with Holm–Sidak corrections for multiple comparisons was applied. *p ≤ 0.05; **p ≤ 0.005.