Wroblewska, A. et al. Cell 175, 1141–1115 (2018).

CRISPR is a versatile tool for gene knockout, activation and repression that has become critical for perturbation screens. Recently, it was shown that it is possible to carry out different perturbations at the single-cell level by using single-cell RNA-seq as a readout, which allows for a dramatic scale-up in the number of targets that can be screened in a single experiment. Phenotyping in these screens has largely been limited to transcriptional profiles. Wroblewska et al. now design protein barcodes (Pro-Codes) consisting of uniquely combined triplet epitopes that are assigned to specific guide RNAs, thus making it possible to use CyTOF mass cytometry to generate multidimensional protein profiles in single-cell pooled CRISPR screens. Each linear epitope can be decoded by a small set of antibodies, which leaves many CyTOF channels available for protein quantification. The authors used Pro-Codes to track tumor cell clonality in mice, and to screen for genes that affect whether breast cancer cells are sensitive to T cell killing.