dc.contributor.author | Dixit, Atray | |
dc.contributor.author | Parnas, Oren | |
dc.contributor.author | Li, Biyu | |
dc.contributor.author | Chen, Jenny | |
dc.contributor.author | Fulco, Charles P. | |
dc.contributor.author | Jerby-Arnon, Livnat | |
dc.contributor.author | Marjanovic, Nemanja D. | |
dc.contributor.author | Dionne, Danielle | |
dc.contributor.author | Burks, Tyler | |
dc.contributor.author | Raychowdhury, Raktima | |
dc.contributor.author | Adamson, Britt | |
dc.contributor.author | Norman, Thomas M. | |
dc.contributor.author | Weissman, Jonathan S. | |
dc.contributor.author | Friedman, Nir | |
dc.contributor.author | Lander, Eric Steven | |
dc.contributor.author | Regev, Aviv | |
dc.date.accessioned | 2018-06-29T19:01:58Z | |
dc.date.available | 2018-06-29T19:01:58Z | |
dc.date.issued | 2016-12 | |
dc.date.submitted | 2016-11 | |
dc.identifier.issn | 0092-8674 | |
dc.identifier.issn | 1097-4172 | |
dc.identifier.uri | http://hdl.handle.net/1721.1/116701 | |
dc.description.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:
single-cell RNA-seq; pooled screen; CRISPR; epistasis; genetic interactions | en_US |
dc.publisher | Elsevier BV | en_US |
dc.relation.isversionof | http://dx.doi.org/10.1016/J.CELL.2016.11.038 | en_US |
dc.rights | Creative Commons Attribution-NonCommercial-NoDerivs License | en_US |
dc.rights.uri | http://creativecommons.org/licenses/by-nc-nd/4.0/ | en_US |
dc.source | PMC | en_US |
dc.title | Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens | en_US |
dc.type | Article | en_US |
dc.identifier.citation | Dixit, Atray et al. “Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.” Cell 167, 7 (December 2016): 1853–1866 © 2016 Elsevier Inc | en_US |
dc.contributor.department | Massachusetts Institute of Technology. Department of Biology | en_US |
dc.contributor.mitauthor | Lander, Eric Steven | |
dc.contributor.mitauthor | Regev, Aviv | |
dc.relation.journal | Cell | en_US |
dc.eprint.version | Author's final manuscript | en_US |
dc.type.uri | http://purl.org/eprint/type/JournalArticle | en_US |
eprint.status | http://purl.org/eprint/status/PeerReviewed | en_US |
dc.date.updated | 2018-06-28T15:38:57Z | |
dspace.orderedauthors | Dixit, Atray; Parnas, Oren; Li, Biyu; Chen, Jenny; Fulco, Charles P.; Jerby-Arnon, Livnat; Marjanovic, Nemanja D.; Dionne, Danielle; Burks, Tyler; Raychowdhury, Raktima; Adamson, Britt; Norman, Thomas M.; Lander, Eric S.; Weissman, Jonathan S.; Friedman, Nir; Regev, Aviv | en_US |
dspace.embargo.terms | N | en_US |
dc.identifier.orcid | https://orcid.org/0000-0001-8567-2049 | |
mit.license | PUBLISHER_CC | en_US |