Direct capture of CRISPR guides enables scalable, multiplexed, and multi-omic Perturb-seq

Joseph M. Replogle; Thomas M. Norman; Albert Xu; Jeffrey A. Hussmann; Jin Chen; J. Zachery Cogan; Elliott J. Meer; Jessica M. Terry; Daniel P. Riordan; Niranjan Srinivas; Ian T. Fiddes; Joseph G. Arthur; Luigi J. Alvarado; Katherine A. Pfeiffer; Tarjei Sigurd Mikkelsen; Jonathan S. Weissman; Britt Adamson

doi:10.1038/s41587-020-0470-y

GenomicsNature BiotechnologyMar 30, 2020

Peer-reviewed journal article

Direct capture of CRISPR guides enables scalable, multiplexed, and multi-omic Perturb-seq

Joseph M. Replogle iD, Thomas M. Norman iD, Albert Xu iD, Jeffrey A. Hussmann iD, Jin Chen iD, J. Zachery Cogan, Elliott J. Meer, Jessica M. Terry, Daniel P. Riordan, Niranjan Srinivas iD, Ian T. Fiddes iD, Joseph G. Arthur iD, Luigi J. Alvarado iD, Katherine A. Pfeiffer, Tarjei Sigurd Mikkelsen iD, Jonathan S. Weissman iD, Britt Adamson iD

Abstract

Pairing CRISPR-based genetic screens with single-cell transcriptional phenotypes (Perturb-seq) has advanced efforts to explore the function of mammalian genes and genetic networks. We present strategies for Perturb-seq that enable direct capture of CRISPR sgRNAs within 3 or 5 single-cell RNA-sequencing libraries using the 10x Genomics platform. This technology greatly expands the accessibility, scalability, and flexibility of Perturb-seq, specifically enabling use with programmed combinatorial perturbations and multiplexing with multi-omic measurements.

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