Fig. 3: Single-cell transcriptome analyses of tumor and immune cells from scrambled and Foxm1 KO groups.

a UMAP representation of 16,552 single cells from scrambled control (6732 cells) and Foxm1 KO (sg1: 4673 and sg3: 5147 cells) samples (n = 5) showing proportions of cell types in the tumor microenvironment. Tumor samples were pooled separately from control and Foxm1 knockout groups for single-cell sequencing. Cell type compositions are shown as cluster numbers (left), samples (middle), and cell type annotation assignments based on marker expression (also see Supp. Data File 1) (right). b Stacked bar plots showing the number of cells in each cell population of scrambled control (Ctrl) and Foxm1 KO (sg1 and sg3) tumors. c Pie chart showing the proportions of different cell populations in scrambled control (Ctrl) and Foxm1 KO (sg1 and sg3) tumors. d UMAP representation of 4483 T and NK cells from control (812 cells) and Foxm1 KO (sg1: 1560 and sg3: 2111) samples (n = 5) showing subpopulations of T and NK cells based on established markers (also see Supp. Data File 2). e T and NK cell subpopulations in scrambled control (Ctrl) and Foxm1 KO (sg1 and sg3) tumors. f Top enriched pathways (GSEA) in T and NK cells from control (Ctrl) and Foxm1 KO (sg1 and sg3) tumors. Normalized enrichment scores (NES) are shown below. g Inflammatory and activation markers in T and NK cells in (ctrl) and Foxm1 KO (sg1 and sg3) tumors. The percent of positive cells is indicated by the size of the dot, and the scaled expression level is indicated by the color. Source data are provided as a Source Data file.