We generated in-house single-cell RNA-Seq data of T cells collected from mouse TNBC tumors of Mal2 overexpression, KD, and control conditions. Raw sequencing data were processed by Cell Ranger for creation of a FASTQ file, alignment to mm10 genome, and generation of a gene expression count matrix. Gene expression was normalized by TPM. Cell clustering analysis was conducted by Seurat v3 with default parameters. Subtypes of T cells were annotated by selected markers as illustrated in Figure 8A (Supplemental Table 3) (6466). Differential gene expression states and relative expression level were computed by using a left truncated mixture Gaussian model. T cell cytotoxicity levels were estimated by the average gene expression level of selected gene markers Ccl4, Cst7, Gzmb, and Ifng. Genes involved in negative and positive regulation of T cell functions were collected from the Gene Ontology database. Standard laboratory practice random procedures were used for cell line groups and mice of the same age and sex. During the evaluation of experiments and results, researchers were not blindly assigned.

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