Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.
Authors | |
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. |
Year of Publication | 2016
|
Journal | Cell
|
Volume | 167
|
Issue | 7
|
Pages | 1853-1866.e17
|
Date Published | 2016 Dec 15
|
ISSN | 1097-4172
|
DOI | 10.1016/j.cell.2016.11.038
|
PubMed ID | 27984732
|
PubMed Central ID | PMC5181115
|
Links | |
Grant list | Howard Hughes Medical Institute / United States
P30 CA014051 / CA / NCI NIH HHS / United States
P50 HG006193 / HG / NHGRI NIH HHS / United States
RM1 HG006193 / HG / NHGRI NIH HHS / United States
|
Additional Materials |