Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens
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; Adamson, Britt; Norman, Thomas M.; Weissman, Jonathan S.; Friedman, Nir; Lander, Eric Steven; Regev, Aviv; ... Show more Show less
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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
Date issued
2016-12Department
Massachusetts Institute of Technology. Department of BiologyJournal
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
ISSN
0092-8674
1097-4172