Single cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis



Hover over data points for cluster assignment and to display menu in top right of plot with additional controls, including snapshot download.

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Hover over data points for cluster assignment and to display menu in top right of plot with additional controls, including snapshot download. Colour of points represents SAVER imputed expression.

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Data description

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.


Data processing

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.


Data availability

Associated raw and processed data are freely available. Please see the related publication:

https://doi.org/10.1038/s41591-018-0078-7