Dataset for "Cell Painting PLUS: Expanding the multiplexing capacity of Cell Painting-based phenotypic profiling using iterative staining-elution cycles"

This data set includes all relevant source data (aggregated and processed profiles) as well as image analysis pipelines (Harmony and Cell Profiler software), KNIME pipelines and R code for data analysis and generation of plots for figures that support the key findings published in: von Coburg E, Wedler M, Muino JM, Wolff C, Körber N, Dunst S, Liu S. Cell Painting PLUS: expanding the multiplexing capacity of Cell Painting-based phenotypic profiling using iterative staining-elution cycles. Nat Commun. 2025 Apr 24;16(1):3857. doi: 10.1038/s41467-025-58765-8. PMID: 40274798; PMCID: PMC12022024. Authors and Affiliations German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), Berlin, Germany Elena von Coburg, Marlene Wedler, Jose M. Muino, Sebastian Dunst & Shu Liu Department of Food Chemistry, University of Potsdam, Potsdam, Germany Elena von Coburg Institute of Biology, Free University of Berlin, Berlin, Germany Marlene Wedler Institute of Clinical Pharmacology and Toxicology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany Jose M. Muino Screening Unit, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany Christopher Wolff Centre for Artificial Intelligence in Public Health Research, Robert Koch Institute, Berlin, Germany Nils Körber Contributions S.L. and S.D. conceived the project and devised the research plan. E.C., M.W. performed the experiments. J.M.M., S.L., S.D., E.C. and M.W. conducted image and data analysis. N.K. established the image registration 4i stitcher software. C.W. generated compound plates and supported image and data analysis. E.C., S.L., and S.D. wrote the main manuscript text, and prepared figures and tables. All authors reviewed the manuscript. Corresponding authors Correspondence to [e-mail] or [e-mail]. Author notes These authors contributed equally: Sebastian Dunst, Shu Liu.