Primary tumours were resected from two triple-negative breast cancer patients. Dissociated cells were FACS sorted to produce a viable population of CD3+ TILs. Single-cell RNA-seq libiraries were prepared with 10X Genomics Chromium Single Cell 3′ Solution and sequenced on HiSeq 2500 High Output Mode using V4 clustering and sequencing chemistry. Raw data were pre-processed with 10X Genomics CellRanger Software to obtain UMI counts. After quality control, 5,759 (4,844+915) cells and 15,621 genes were retained for downstream analysis.
Unimputed data is normalized for library size with Seurat default method. Imputed data is normalized within SAVER. For feature t-SNE plots, data is log-transformed with offset 0.1. For violin plots, data is log-transformed with offset 1.
Associated raw and processed data are freely available. Please see the related publication:https://doi.org/10.1038/s41591-018-0078-7