Title | Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. |
Publication Type | Journal Article |
Year of Publication | 2016 |
Authors | Dixit, A, Parnas, O, Li, B, Chen, J, Fulco, CP, Jerby-Arnon, L, Marjanovic, ND, Dionne, D, Burks, T, Raychowdhury, R, Adamson, B, Norman, TM, Lander, ES, Weissman, JS, Friedman, N, Regev, iv, A |
Journal | Cell |
Volume | 167 |
Issue | 7 |
Pagination | 1853-1866.e17 |
Date Published | 2016 Dec 15 |
ISSN | 1097-4172 |
Keywords | Animals, Cell Cycle, Clustered Regularly Interspaced Short Palindromic Repeats, Feedback, Gene Expression Profiling, Gene Knockdown Techniques, Humans, K562 Cells, Mice, Mice, Transgenic, Sequence Analysis, RNA, Single-Cell Analysis, Transcription Factors |
Abstract | <p>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.</p> |
DOI | 10.1016/j.cell.2016.11.038 |
Alternate Journal | Cell |
PubMed ID | 27984732 |
PubMed Central ID | PMC5181115 |
Grant List | P30 CA014051 / CA / NCI NIH HHS / United States R01 DA036858 / DA / NIDA NIH HHS / United States R01 AG041826 / AG / NIA NIH HHS / United States P50 HG006193 / HG / NHGRI NIH HHS / United States RM1 HG006193 / HG / NHGRI NIH HHS / United States / HHMI_ / Howard Hughes Medical Institute / United States |