Single cell mapping of breast tumor stroma reveals dynamically evolving compositions of cancer-associated fibroblasts along tumor progression (bulk RNA-seq dataset)

Tumors are complex ecosystems, in which malignant and non-malignant cells engage in continuous interactions. Cancer associated fibroblasts (CAFs) are the most abundant non-malignant cells in the majority of carcinomas. The wide range of activities that CAFs perform suggests a dynamic and heterogeneous composition, yet tumor infiltrating CAF subpopulations remain poorly characterized. Here we used single cell RNA sequencing and index sorting to map CAFs at various stages of tumor progression and metastasis. BALB/c female mice were orthotopically injected with 4T1-luc cells into the mammary pat pad. Tumors were harvested two weeks or four weeks following the injection. Mammary tissue was harvested from naïve mice (normal mammary fat pad), and lung metastases were harvested five weeks after the injection. The tissues were then dissociated and single-cell sorted for MARS-sequencing, using the follwing gating strategy to select for stromal cells: PI- /Ter119-/ CD45-/ EpCAM-.