JUMP Cell Painting dataset: morphological impact of 136,000 chemical and genetic perturbations. Chandrasekaran, S. N., Ackerman, J., Alix, E., Ando, D. M., Arevalo, J., Bennion, M., Boisseau, N., Borowa, A., Boyd, J. D., Brino, L., Byrne, P. J., Ceulemans, H., Ch’ng, C., Cimini, B. A., Clevert, D., Deflaux, N., Doench, J. G., Dorval, T., Doyonnas, R., Dragone, V., Engkvist, O., Faloon, P. W., Fritchman, B., Fuchs, F., Garg, S., Gilbert, T. J., Glazer, D., Gnutt, D., Goodale, A., Grignard, J., Guenther, J., Han, Y., Hanifehlou, Z., Hariharan, S., Hernandez, D., Horman, S. R., Hormel, G., Huntley, M., Icke, I., Iida, M., Jacob, C. B., Jaensch, S., Khetan, J., Kost-Alimova, M., Krawiec, T., Kuhn, D., Lardeau, C., Lembke, A., Lin, F., Little, K. D., Lofstrom, K. R., Lotfi, S., Logan, D. J., Luo, Y., Madoux, F., Zapata, P. A. M., Marion, B. A., Martin, G., McCarthy, N. J., Mervin, L., Miller, L., Mohamed, H., Monteverde, T., Mouchet, E., Nicke, B., Ogier, A., Ong, A., Osterland, M., Otrocka, M., Peeters, P. J., Pilling, J., Prechtl, S., Qian, C., Rataj, K., Root, D. E., Sakata, S. K., Scrace, S., Shimizu, H., Simon, D., Sommer, P., Spruiell, C., Sumia, I., Swalley, S. E., Terauchi, H., Thibaudeau, A., Unruh, A., Waeter, J. V. d., Dyck, M. V., Staden, C. v., Warchoł, M., Weisbart, E., Weiss, A., Wiest-Daessle, N., Williams, G., Yu, S., Zapiec, B., Żyła, M., Singh, S., & Carpenter, A. E. March, 2023. Pages: 2023.03.23.534023 Section: New Results![JUMP Cell Painting dataset: morphological impact of 136,000 chemical and genetic perturbations [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex 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/.
@misc{chandrasekaran_jump_2023,
title = {{JUMP} {Cell} {Painting} dataset: morphological impact of 136,000 chemical and genetic perturbations},
copyright = {© 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
shorttitle = {{JUMP} {Cell} {Painting} dataset},
url = {https://www.biorxiv.org/content/10.1101/2023.03.23.534023v2},
doi = {10.1101/2023.03.23.534023},
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/.},
language = {en},
urldate = {2023-11-28},
publisher = {bioRxiv},
author = {Chandrasekaran, Srinivas Niranj and Ackerman, Jeanelle and Alix, Eric and Ando, D. Michael and Arevalo, John and Bennion, Melissa and Boisseau, Nicolas and Borowa, Adriana and Boyd, Justin D. and Brino, Laurent and Byrne, Patrick J. and Ceulemans, Hugo and Ch’ng, Carolyn and Cimini, Beth A. and Clevert, Djork-Arne and Deflaux, Nicole and Doench, John G. and Dorval, Thierry and Doyonnas, Regis and Dragone, Vincenza and Engkvist, Ola and Faloon, Patrick W. and Fritchman, Briana and Fuchs, Florian and Garg, Sakshi and Gilbert, Tamara J. and Glazer, David and Gnutt, David and Goodale, Amy and Grignard, Jeremy and Guenther, Judith and Han, Yu and Hanifehlou, Zahra and Hariharan, Santosh and Hernandez, Desiree and Horman, Shane R. and Hormel, Gisela and Huntley, Michael and Icke, Ilknur and Iida, Makiyo and Jacob, Christina B. and Jaensch, Steffen and Khetan, Jawahar and Kost-Alimova, Maria and Krawiec, Tomasz and Kuhn, Daniel and Lardeau, Charles-Hugues and Lembke, Amanda and Lin, Francis and Little, Kevin D. and Lofstrom, Kenneth R. and Lotfi, Sofia and Logan, David J. and Luo, Yi and Madoux, Franck and Zapata, Paula A. Marin and Marion, Brittany A. and Martin, Glynn and McCarthy, Nicola Jane and Mervin, Lewis and Miller, Lisa and Mohamed, Haseeb and Monteverde, Tiziana and Mouchet, Elizabeth and Nicke, Barbara and Ogier, Arnaud and Ong, Anne-Laure and Osterland, Marc and Otrocka, Magdalena and Peeters, Pieter J. and Pilling, James and Prechtl, Stefan and Qian, Chen and Rataj, Krzysztof and Root, David E. and Sakata, Sylvie K. and Scrace, Simon and Shimizu, Hajime and Simon, David and Sommer, Peter and Spruiell, Craig and Sumia, Iffat and Swalley, Susanne E. and Terauchi, Hiroki and Thibaudeau, Amandine and Unruh, Amy and Waeter, Jelle Van de and Dyck, Michiel Van and Staden, Carlo van and Warchoł, Michał and Weisbart, Erin and Weiss, Amélie and Wiest-Daessle, Nicolas and Williams, Guy and Yu, Shan and Zapiec, Bolek and Żyła, Marek and Singh, Shantanu and Carpenter, Anne E.},
month = mar,
year = {2023},
note = {Pages: 2023.03.23.534023
Section: New Results},
file = {Full Text PDF:/Users/flodje_uds/Zotero/storage/GFKJM6LS/Chandrasekaran et al. - 2023 - JUMP Cell Painting dataset morphological impact o.pdf:application/pdf},
}
Downloads: 0
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This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},\n\tshorttitle = {{JUMP} {Cell} {Painting} dataset},\n\turl = {https://www.biorxiv.org/content/10.1101/2023.03.23.534023v2},\n\tdoi = {10.1101/2023.03.23.534023},\n\tabstract = {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. 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Michael and Arevalo, John and Bennion, Melissa and Boisseau, Nicolas and Borowa, Adriana and Boyd, Justin D. and Brino, Laurent and Byrne, Patrick J. and Ceulemans, Hugo and Ch’ng, Carolyn and Cimini, Beth A. and Clevert, Djork-Arne and Deflaux, Nicole and Doench, John G. and Dorval, Thierry and Doyonnas, Regis and Dragone, Vincenza and Engkvist, Ola and Faloon, Patrick W. and Fritchman, Briana and Fuchs, Florian and Garg, Sakshi and Gilbert, Tamara J. and Glazer, David and Gnutt, David and Goodale, Amy and Grignard, Jeremy and Guenther, Judith and Han, Yu and Hanifehlou, Zahra and Hariharan, Santosh and Hernandez, Desiree and Horman, Shane R. and Hormel, Gisela and Huntley, Michael and Icke, Ilknur and Iida, Makiyo and Jacob, Christina B. and Jaensch, Steffen and Khetan, Jawahar and Kost-Alimova, Maria and Krawiec, Tomasz and Kuhn, Daniel and Lardeau, Charles-Hugues and Lembke, Amanda and Lin, Francis and Little, Kevin D. and Lofstrom, Kenneth R. and Lotfi, Sofia and Logan, David J. and Luo, Yi and Madoux, Franck and Zapata, Paula A. Marin and Marion, Brittany A. and Martin, Glynn and McCarthy, Nicola Jane and Mervin, Lewis and Miller, Lisa and Mohamed, Haseeb and Monteverde, Tiziana and Mouchet, Elizabeth and Nicke, Barbara and Ogier, Arnaud and Ong, Anne-Laure and Osterland, Marc and Otrocka, Magdalena and Peeters, Pieter J. and Pilling, James and Prechtl, Stefan and Qian, Chen and Rataj, Krzysztof and Root, David E. and Sakata, Sylvie K. and Scrace, Simon and Shimizu, Hajime and Simon, David and Sommer, Peter and Spruiell, Craig and Sumia, Iffat and Swalley, Susanne E. and Terauchi, Hiroki and Thibaudeau, Amandine and Unruh, Amy and Waeter, Jelle Van de and Dyck, Michiel Van and Staden, Carlo van and Warchoł, Michał and Weisbart, Erin and Weiss, Amélie and Wiest-Daessle, Nicolas and Williams, Guy and Yu, Shan and Zapiec, Bolek and Żyła, Marek and Singh, Shantanu and Carpenter, Anne E.},\n\tmonth = mar,\n\tyear = {2023},\n\tnote = {Pages: 2023.03.23.534023\nSection: New Results},\n\tfile = {Full Text PDF:/Users/flodje_uds/Zotero/storage/GFKJM6LS/Chandrasekaran et al. - 2023 - JUMP Cell Painting dataset morphological impact o.pdf:application/pdf},\n}\n\n","author_short":["Chandrasekaran, S. 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E."],"key":"chandrasekaran_jump_2023","id":"chandrasekaran_jump_2023","bibbaseid":"chandrasekaran-ackerman-alix-ando-arevalo-bennion-boisseau-borowa-etal-jumpcellpaintingdatasetmorphologicalimpactof136000chemicalandgeneticperturbations-2023","role":"author","urls":{"Paper":"https://www.biorxiv.org/content/10.1101/2023.03.23.534023v2"},"metadata":{"authorlinks":{}}},"bibtype":"misc","biburl":"https://bibbase.org/network/files/H3SAh2KLDwd2dQGtm","dataSources":["5kE2CnMg6u7MRd5WC","Bh4soD3jyHYoSp98p"],"keywords":[],"search_terms":["jump","cell","painting","dataset","morphological","impact","136","000","chemical","genetic","perturbations","chandrasekaran","ackerman","alix","ando","arevalo","bennion","boisseau","borowa","boyd","brino","byrne","ceulemans","ch’ng","cimini","clevert","deflaux","doench","dorval","doyonnas","dragone","engkvist","faloon","fritchman","fuchs","garg","gilbert","glazer","gnutt","goodale","grignard","guenther","han","hanifehlou","hariharan","hernandez","horman","hormel","huntley","icke","iida","jacob","jaensch","khetan","kost-alimova","krawiec","kuhn","lardeau","lembke","lin","little","lofstrom","lotfi","logan","luo","madoux","zapata","marion","martin","mccarthy","mervin","miller","mohamed","monteverde","mouchet","nicke","ogier","ong","osterland","otrocka","peeters","pilling","prechtl","qian","rataj","root","sakata","scrace","shimizu","simon","sommer","spruiell","sumia","swalley","terauchi","thibaudeau","unruh","waeter","dyck","staden","warchoł","weisbart","weiss","wiest-daessle","williams","yu","zapiec","żyła","singh","carpenter"],"title":"JUMP Cell Painting dataset: morphological impact of 136,000 chemical and genetic perturbations","year":2023}