Optimised, frameshift-driven design for single-cell CRISPR perturbation screens

CRISPR-Cas9 has been widely used to functionally interrogate multiple aspects of cellular physiology and pathophysiology from single gene studies to genome-wide screens. Proper design of highly efficient guide RNAs directing the CRISPR genome editing process is critical for success in these types of experiments. Here, we present a pipeline for designing highly efficient loss-of-function guide RNA (gRNA) libraries with improved rates of knock-out efficiency compared to previous guide RNA library designs. We provide pre-computed and triaged gRNAs from our pipeline for all human and mouse transcripts through a fully searchable online portal as a resource to the community. Overall design: 13 Key regulators of the Oestrogen Receptor (ER) complex in MCF7 breast cancer cells were perturbed using CRISPR in duplicate experiments and analysed using scRNAseq