Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens
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nihms835459.pdf
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Author(s)
Dixit, Atray
Parnas, Oren
Li, Biyu
Chen, Jenny
Fulco, Charles P.
Jerby-Arnon, Livnat
Marjanovic, Nemanja D.
Dionne, Danielle
Burks, Tyler
Raychowdhury, Raktima
Date Issued
December 2016
Journal
Cell
Publisher
Elsevier BV
Citation
Dixit, Atray et al. “Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.” Cell 167, 7 (December 2016): 1853–1866 © 2016 Elsevier Inc
Version
Author's final manuscript
Abstract
Genetic screens help infer gene function in mammalian cells, but it has remained difficult to assay complex phenotypes—such as transcriptional profiles—at scale. Here, we develop Perturb-seq, combining single-cell RNA sequencing (RNA-seq) and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations to perform many such assays in a pool. We demonstrate Perturb-seq by analyzing 200,000 cells in immune cells and cell lines, focusing on transcription factors regulating the response of dendritic cells to lipopolysaccharide (LPS). Perturb-seq accurately identifies individual gene targets, gene signatures, and cell states affected by individual perturbations and their genetic interactions. We posit new functions for regulators of differentiation, the anti-viral response, and mitochondrial function during immune activation. By decomposing many high content measurements into the effects of perturbations, their interactions, and diverse cell metadata, Perturb-seq dramatically increases the scope of pooled genomic assays. Keywords:
single-cell RNA-seq; pooled screen; CRISPR; epistasis; genetic interactions
MIT Department
Massachusetts Institute of Technology. Department of Biology
Terms of Use
Creative Commons Attribution-NonCommercial-NoDerivs License
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DOI of Published Version
https://doi.org/10.1016/J.CELL.2016.11.038
