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.-A.; 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,

doi:10.1101/2023.03.23.534023

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bioRxiv · 10.1101/2023.03.23.534023

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

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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/.

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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.-A., 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,. 2023-03-24. JUMP Cell Painting dataset: morphological impact of 136,000 chemical and genetic perturbations. https://doi.org/10.1101/2023.03.23.534023

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