A genome-wide atlas of human cell morphology.

Journal

bioRxiv : the preprint server for biology
Titre abrégé: bioRxiv
Pays: United States
ID NLM: 101680187

Informations de publication

Date de publication:
07 Aug 2023
Historique:
pubmed: 23 8 2023
medline: 23 8 2023
entrez: 23 8 2023
Statut: epublish

Résumé

A key challenge of the modern genomics era is developing data-driven representations of gene function. Here, we present the first unbiased morphology-based genome-wide perturbation atlas in human cells, containing three genome-scale genotype-phenotype maps comprising >20,000 single-gene CRISPR-Cas9-based knockout experiments in >30 million cells. Our optical pooled cell profiling approach (PERISCOPE) combines a de-stainable high-dimensional phenotyping panel (based on Cell Painting

Identifiants

DOI: 10.1101/2023.08.06.552164 PMID: 37609130 PMC: PMC10441312
pubmed: 37609130
doi: 10.1101/2023.08.06.552164
pmc: PMC10441312
pii:
doi:

Types de publication

Preprint

Langues

eng

Subventions

Organisme : NIGMS NIH HHS
ID : DP2 GM146252
Pays : United States

Déclaration de conflit d'intérêts

Conflicts of interest C.H.J. and J.Y. are employees of Calico Life Sciences LLC. S.S. and A.E.C. serve as scientific advisors for companies that use image-based profiling and Cell Painting (A.E.C: Recursion, SyzOnc, S.S.: Waypoint Bio, Dewpoint Therapeutics) and receive honoraria for occasional talks at pharmaceutical and biotechnology companies. P.C.B. is a consultant to or holds equity in 10X Genomics, General Automation Lab Technologies/Isolation Bio, Celsius Therapeutics, Next Gen Diagnostics, Cache DNA, Concerto Biosciences, Stately, Ramona Optics, Bifrost Biosystems, and Amber Bio. P.C.B.’s laboratory receives research funding from Merck and Genentech for work related to genetic screening. The Broad Institute and MIT may seek to commercialize aspects of this work, and related applications for intellectual property have been filed including WO2019222284A1 In situ cell screening methods and systems. All other authors declare no competing interests.

Auteurs

Meraj Ramezani (M)

Broad Institute of MIT & Harvard, Cambridge, MA, USA.
Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Julia Bauman (J)

Broad Institute of MIT & Harvard, Cambridge, MA, USA.
Current address: Stanford University, Stanford, CA, USA.

Avtar Singh (A)

Broad Institute of MIT & Harvard, Cambridge, MA, USA.
Current address: Genentech Department of Cellular and Tissue Genomics, South San Francisco, CA, USA.

Erin Weisbart (E)

Broad Institute of MIT & Harvard, Cambridge, MA, USA.

John Yong (J)

Calico Life Sciences LLC, South San Francisco, CA, USA.

Maria Lozada (M)

Broad Institute of MIT & Harvard, Cambridge, MA, USA.
Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Gregory P Way (GP)

Broad Institute of MIT & Harvard, Cambridge, MA, USA.
Current address: Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA.

Sanam L Kavari (SL)

Broad Institute of MIT & Harvard, Cambridge, MA, USA.
Current address: University of Pennsylvania, Philadelphia, PA, USA.

Celeste Diaz (C)

Broad Institute of MIT & Harvard, Cambridge, MA, USA.
Current address: Stanford University, Stanford, CA, USA.

Marzieh Haghighi (M)

Broad Institute of MIT & Harvard, Cambridge, MA, USA.

Thiago M Batista (TM)

Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA.
The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at Broad Institute, Cambridge, MA, USA.

Joaquín Pérez-Schindler (J)

Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA.
The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at Broad Institute, Cambridge, MA, USA.

Melina Claussnitzer (M)

Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA.
The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at Broad Institute, Cambridge, MA, USA.
Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.

Shantanu Singh (S)

Broad Institute of MIT & Harvard, Cambridge, MA, USA.

Beth A Cimini (BA)

Broad Institute of MIT & Harvard, Cambridge, MA, USA.

Paul C Blainey (PC)

Broad Institute of MIT & Harvard, Cambridge, MA, USA.
MIT Department of Biological Engineering, Cambridge, MA, USA.
Koch Institute for Integrative Research at MIT, Cambridge, MA, USA.

Anne E Carpenter (AE)

Broad Institute of MIT & Harvard, Cambridge, MA, USA.

Calvin H Jan (CH)

Calico Life Sciences LLC, South San Francisco, CA, USA.

James T Neal (JT)

Broad Institute of MIT & Harvard, Cambridge, MA, USA.
Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA.
The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at Broad Institute, Cambridge, MA, USA.

Classifications MeSH