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