Evidence map›Paper›PMID 27984732›Full record

ArticleCell2016

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

Atray Dixit, Oren Parnas, Biyu Li, Jenny Chen, Charles P Fulco, Livnat Jerby-Arnon, Nemanja D Marjanovic, Danielle Dionne, Tyler Burks, Raktima Raychowdhury and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,092 papers.

0numbers the graph read from it
0cells of the map it votes in
1,092citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1,092 citing papers in PubMed.

  1. CRISPR/Cas Systems: Biological Basis and Genome Editing Applications.Methods in molecular biology (Clifton, N.J.) · 2027
    Review
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1,032 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

16 authors.

Atray DixitBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA.
Oren ParnasBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Biyu LiBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Jenny ChenBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA.
Charles P FulcoBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
Livnat Jerby-ArnonBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Nemanja D MarjanovicBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.
Danielle DionneBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Tyler BurksBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Raktima RaychowdhuryBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Britt AdamsonDepartment of Cellular and Molecular Pharmacology, California Institute of Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
Thomas M NormanDepartment of Cellular and Molecular Pharmacology, California Institute of Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
Eric S LanderBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.
Jonathan S WeissmanDepartment of Cellular and Molecular Pharmacology, California Institute of Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
Nir FriedmanBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; School of Engineering and Computer Science and Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
Aviv RegevBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address: aregev@broadinstitute.org.

Funding

VIRUS PRODUCTION COREP30CA014051 · NCI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI MATTHEW G. VANDER HEIDEN · 1985 to 2026
$93.9M
Center for Cell CircuitsP50HG006193 · NHGRI · BROAD INSTITUTE, INC. · PI REGEV, AVIV · 2011 to 2015
$15.6M
Center for Cell CircuitsRM1HG006193 · NHGRI · BROAD INSTITUTE, INC. · PI BLAINEY, PAUL CLARK, HACOHEN, NIR · 2016 to 2020
$14.9M
Harnessing CRISPR for Targeted and Inducible Epigenomic ReprogrammingR01DA036858 · NIDA · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LIM, WENDELL A, QI, LEI STANLEY · 2013 to 2017
$2.9M
Human Gene Knockdowns that May Extend LifespanR01AG041826 · NIA · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI WEISSMAN, JONATHAN S. · 2012 to 2016
$1.6M
Howard Hughes Medical InstituteNCI NIH HHS P30 CA014051NHGRI NIH HHS P50 HG006193NHGRI NIH HHS RM1 HG006193NIA NIH HHS R01 AG041826NIDA NIH HHS R01 DA036858
6 · The paper itself

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.

Indexed as

AnimalsCell CycleClustered Regularly Interspaced Short Palindromic RepeatsFeedbackGene Expression ProfilingGene Knockdown TechniquesHumansK562 CellsMiceMice, TransgenicSequence Analysis, RNASingle-Cell AnalysisTranscription FactorsTranscription FactorsCRISPRepistasisgenetic interactionspooled screensingle-cell RNA-seq

Identifiers

PMID27984732
PMCPMC5181115

What OpenQuestion holds

Textmetadata
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Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.