Dataset for "Cell Painting PLUS: An iterative staining-elution protocol for high-content phenotypic screenings"

This data set includes all relevant source data for the publication Wedler et al. (2026) Cell Painting PLUS: An iterative staining-elution protocol for high-content phenotypic screenings (Current Protocols, doi:10.1002/cpz1.70368 ).These data were generated from a Cell Painting PLUS (CPP) screen performed in U2OS cells and published in von Coburg et al. 2025 (https://doi.org/10.1038/s41467-025-58765-8). The CPP images of U2OS cells were analyzed using a customized Harmony (Revvity Inc.) analysis pipeline specifically developed for CPP data. This pipeline is publicly available as Supplementary Data 19 in von Coburg et al. 2025 (https://doi.org/10.5281/zenodo.14982928) and includes the Add Channel 4i application-specific building block (ABB) for image registration (Kirsch (2025), https://doi.org/10.5281/zenodo.15119993).The data set Harmony_image_analysis_results.zip contains the exported result files from the image analysis, including per-object measurements that capture morphological features for each individual cell. Each folder corresponds to the measurement of one plate, representing an independent biological replicate. These data are the output files of the image analysis and have not been standardized or filtered. The file Compound_layout.xlsx provides details on the plate layout, including the tested compounds and their concentrations. The file Table_to_exclude_wells.xlsx lists wells that should be omitted from downstream analyses due to technical issues such as pipetting errors. Each plate was imaged using five fields per well and two optical sections (z-planes); the analyzed z-plane for each plate is specified in Table_planes.xlsx. This dataset can be used as an input for the CPPAnalyzer Jupyter notebook (available at Wedler et al., 2026, https://doi.org/10.5281/zenodo.18385218) to normalize and standardize the data for subsequent analysis.The data set normalized_data.zip includes the data that were normalized using the CPPAnalyzer Jupyter notebook with settings as in 251219_U2OS.ipynb.The normalized data can be used as an input for the CPPManager KNIME workflow (available at Wedler et al (2026), https://doi.org/10.5281/zenodo.18385218).The files Fig1, Fig2 and Fig3 contain the source data used to generate the figures for Wedler et al. (2026) "Cell Painting PLUS: An iterative staining-elution protocol for high-content phenotypic screenings" (Current Protocols, doi:10.1002/cpz1.70368 ).