Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.

TitlePerturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.
Publication TypeJournal Article
Year of Publication2016
AuthorsDixit, 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
JournalCell
Volume167
Issue7
Pagination1853-1866.e17
Date Published2016 Dec 15
ISSN1097-4172
KeywordsAnimals, 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

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.

DOI10.1016/j.cell.2016.11.038
Alternate JournalCell
PubMed ID27984732
PubMed Central IDPMC5181115
Grant ListP30 CA014051 / CA / NCI NIH HHS / United States
R01 DA036858 / DA / NIDA NIH HHS / United States
/ / Howard Hughes Medical Institute / 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