Data generation and preprocessing

We collected cells from four tumor samples and three healthy control mouse samples. The single-cell RNA-seq samples were processed according to the 10× Genomics protocol. Cell Ranger Single-Cell Software Suite (version 6.0.0, 10× Genomics, using the option –include-introns) was used to quality control and quantify the single-cell expression data to generate filtered gene-barcode matrices for 90,715 cells with an average of 3037 mRNA molecules (UMIs, median: 1963, range: 302–32,765). Cells with low (≤500) UMI counts or more than 20% UMI counts from mitochondrial genes were considered low quality as proportion of mitochondrial genes may indicate the quality of cells¹³⁹. With this quality control criterion, 9.3% of cells were considered low-quality (9.7% of low-quality cells from the control group and 9.2% of low-quality cells in the tumor group).