JUMP Cell Painting dataset: morphological impact of 136,000 chemical and genetic perturbations

Srinivas Niranj Chandrasekaran(Broad Institute), Jeanelle Ackerman(Broad Institute), Eric Alix(Horizon Discovery (United Kingdom)), D. Michael Ando(Google (United States)), John Arévalo(Broad Institute), Melissa Bennion(Biogen (United States)), Nicolas Boisseau(Institut Rayonnement-Matière de Saclay), Adriana Borowa, Justin D. Boyd(Pfizer (United States)), Laurent Brino, Patrick J. Byrne(Broad Institute), Hugo Ceulemans(Janssen (Belgium)), Carolyn Ch’ng(Amgen (Canada)), Beth A. Cimini(Broad Institute), Djork-Arné Clevert(Bayer (Germany)), Nicole Deflaux, John G. Doench(Broad Institute), Thierry Dorval(Institut Rayonnement-Matière de Saclay), Régis Doyonnas(Pfizer (United States)), Vincenza Dragone(Merck KGaA, Darmstadt (Germany)), Ola Engkvist(AstraZeneca (Sweden)), Patrick W. Faloon(Biogen (United States)), Briana Fritchman(Broad Institute), Florian Fuchs(Nuvisan (Germany)), Sakshi Garg(Merck KGaA, Darmstadt (Germany)), Tamara J. Gilbert(Pfizer (United States)), David Glazer, David Gnutt(Bayer (Germany)), Amy Goodale(Broad Institute), Jeremy Grignard(Institut Rayonnement-Matière de Saclay), Judith Guenther(Bayer (Germany)), Yu Han(Broad Institute), Zahra Hanifehlou, Santosh Hariharan(Pfizer (United States)), Desiree Hernandez(Broad Institute), Shane R. Horman(Takeda (United States)), Gisela Hormel(Merck KGaA, Darmstadt (Germany)), Michael Huntley(Amgen (United States)), Ilknur Icke(Takeda (United States)), Makiyo Iida(Eisai (Japan)), Christina Gros, Steffen Jaensch(Janssen (Belgium)), Jawahar Khetan(Amgen (United States)), Maria Kost‐Alimova(Broad Institute), Tomasz Krawiec, Daniel Kühn(Merck KGaA, Darmstadt (Germany)), Charles-Hugues Lardeau(Janssen (Belgium)), Amanda Lembke(Amgen (United States)), Francis Lin(Amgen (United States)), Kevin D. Little(Biogen (United States)), Kenneth R. Lofstrom(Biogen (United States)), Sofia Lotfi(Institut Rayonnement-Matière de Saclay), David J. Logan(Pfizer (United States)), Yi Luo(Takeda (United States)), Franck Madoux(Amgen (United States)), Paula Andrea Marin Zapata(Bayer (Germany)), Brittany A. Marion(Broad Institute), Glynn Martin(Horizon Discovery (United Kingdom)), Nicola McCarthy(Horizon Discovery (United Kingdom)), Lewis Mervin(AstraZeneca (United Kingdom)), Lisa Miller(Broad Institute), Haseeb Mohamed(Amgen (United States)), Tiziana Monteverde(AstraZeneca (United Kingdom)), Elizabeth Mouchet(AstraZeneca (United Kingdom)), Barbara Nicke(Bayer (Germany)), Arnaud Ogier, Anne-Laure Ong(Institut Rayonnement-Matière de Saclay), Marc Osterland(Bayer (Germany)), Magdalena Otrocka, Pieter J. Peeters(Janssen (Belgium)), James Pilling(AstraZeneca (United Kingdom)), Stefan Prechtl(Bayer (Germany)), Qian Chen(AstraZeneca (United Kingdom)), Krzysztof Rataj, David E. Root(Broad Institute), Sylvie K. Sakata(Pfizer (United States)), Simon Scrace(Horizon Discovery (United Kingdom)), Hajime Shimizu(Eisai (Japan)), David Simón(Amgen (United States)), Peter Sommer, Craig Spruiell(Amgen (United States)), Iffat Sumia(Institut Rayonnement-Matière de Saclay), Susanne E. Swalley(Biogen (United States)), Hiroki Terauchi(Eisai (Japan)), Amandine Thibaudeau, Amy Unruh, Jelle Van de Waeter, Michiel Van Dyck(Janssen (Belgium)), Carlo van Staden(Amgen (United States)), Michał Warchoł, Erin Weisbart(Broad Institute), Amélie Weiss, Nicolas Wiest-Daesslé, Guy Williams(AstraZeneca (United Kingdom)), Shan Yu(Takeda (United States)), Bolek Zapiec(Merck KGaA, Darmstadt (Germany)), Marek Żyła, Shantanu Singh(Broad Institute), Anne E. Carpenter(Broad Institute)
bioRxiv (Cold Spring Harbor Laboratory)
March 24, 2023
10.1101/2023.03.23.534023
Cited by 100Open Access
Full Text

Abstract

Abstract Image-based profiling has emerged as a powerful technology for various steps in basic biological and pharmaceutical discovery, but the community has lacked a large, public reference set of data from chemical and genetic perturbations. Here we present data generated by the Joint Undertaking for Morphological Profiling (JUMP)-Cell Painting Consortium, a collaboration between 10 pharmaceutical companies, six supporting technology companies, and two non-profit partners. When completed, the dataset will contain images and profiles from the Cell Painting assay for over 116,750 unique compounds, over-expression of 12,602 genes, and knockout of 7,975 genes using CRISPR-Cas9, all in human osteosarcoma cells (U2OS). The dataset is estimated to be 115 TB in size and capturing 1.6 billion cells and their single-cell profiles. File quality control and upload is underway and will be completed over the coming months at the Cell Painting Gallery: https://registry.opendata.aws/cellpainting-gallery . A portal to visualize a subset of the data is available at https://phenaid.ardigen.com/jumpcpexplorer/ .

Related Papers

No related papers found

Powered by citation graph analysis