On the Design of CRISPR-based Single-cell Molecular Screens

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2018 Feb 20

PMID 29457792

Citations 114

Authors

Andrew J Hill

Jose L McFaline-Figueroa

Lea M Starita

Molly J Gasperini

Kenneth A Matreyek

Jonathan Packer

Dana Jackson

Jay Shendure

Cole Trapnell

Affiliations

Soon will be listed here.

Abstract

Several groups recently coupled CRISPR perturbations and single-cell RNA-seq for pooled genetic screens. We demonstrate that vector designs of these studies are susceptible to ∼50% swapping of guide RNA-barcode associations because of lentiviral template switching. We optimized a published alternative, CROP-seq, in which the guide RNA also serves as the barcode, and here confirm that this strategy performs robustly and doubled the rate at which guides are assigned to cells to 94%.

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