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.本数据集涵盖所有相关源数据（经聚合与处理的样本概况），以及用于数据分析与论文附图绘图生成的图像分析流程（Harmony与Cell Profiler软件）、KNIME流程与R代码，上述材料可支撑发表于以下论文的核心研究发现： von Coburg E, Wedler M, Muino JM, Wolff C, Körber N, Dunst S, Liu S. 细胞绘画PLUS（Cell Painting PLUS）：通过迭代染色-洗脱循环拓展基于细胞绘画（Cell Painting）的表型分析的多重检测能力. 自然·通讯. 2025年4月24日;16(1):3857. DOI: 10.1038/s41467-025-58765-8，PMID: 40274798；PMCID: PMC12022024. 作者与所属机构 德国联邦风险评估研究所（BfR）实验动物保护德国中心（Bf3R），德国柏林 Elena von Coburg、Marlene Wedler、Jose M. Muino、Sebastian Dunst 与 Shu Liu 波茨坦大学食品化学系，德国波茨坦 Elena von Coburg 柏林自由大学生物学研究所，德国柏林 Marlene Wedler 夏里特——柏林大学医学院（柏林自由大学、柏林洪堡大学附属成员机构，柏林健康研究所）临床药理学与毒理学研究所，德国柏林 Jose M. Muino 莱布尼茨分子药理学研究所（FMP）筛选单元，德国柏林 Christopher Wolff 罗伯特·科赫研究所公共卫生人工智能研究中心，德国柏林 Nils Körber 贡献 S.L.与S.D.构思本项目并设计研究方案。E.C.、M.W.开展实验工作。J.M.M.、S.L.、S.D.、E.C.与M.W.完成图像与数据分析。N.K.开发了图像配准4i stitcher软件。C.W.制备化合物板并协助图像与数据分析。E.C.、S.L.与S.D.撰写论文主体文本，并制作图表与表格。全体作者均审阅了本文稿。 通讯作者 通讯邮箱：[e-mail] 或 [e-mail]。 作者注 本文共同第一作者：Sebastian Dunst、Shu Liu。