Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Author Atray Dixit, Oren Parnas, Biyu Li, Jenny Chen, Charles Fulco, Livnat Jerby-Arnon, Nemanja Marjanovic, Danielle Dionne, Tyler Burks, Raktima Raychowdhury, Britt Adamson, Thomas Norman, Eric Lander, Jonathan Weissman, Nir Friedman, Aviv Regev Publication Year 2016 Type Journal Article 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 CRISPR, epistasis, genetic interactions, pooled screen, Single-cell RNA-seq Journal Cell Volume 167 Issue 7 Pages 1853-1866.e17 Date Published 12/2016 ISSN Number 1097-4172 DOI 10.1016/j.cell.2016.11.038 Alternate Journal Cell PMCID PMC5181115 PMID 27984732 PubMedPubMed CentralGoogle ScholarBibTeXEndNote X3 XML