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 ).本数据集涵盖了Wedler等人（2026年）发表的论文《细胞绘画PLUS（Cell Painting PLUS）：高内涵表型筛选的迭代染色-洗脱方案》（发表于《Current Protocols》，DOI:10.1002/cpz1.70368）所需的全部相关源数据。 这些数据源自于在U2OS细胞中开展的Cell Painting PLUS（CPP）筛选实验，并发表于von Coburg等人2025年的研究（https://doi.org/10.1038/s41467-025-58765-8）。 针对U2OS细胞的CPP成像数据，采用专为CPP数据开发的定制化Harmony（Revvity公司）分析流程进行解析。该分析流程作为补充数据19公开于von Coburg等人2025年的研究（https://doi.org/10.5281/zenodo.14982928），其中包含用于图像配准的Add Channel 4i 专用构建模块（application-specific building block，ABB，Kirsch，2025年，https://doi.org/10.5281/zenodo.15119993）。 数据集Harmony_image_analysis_results.zip 包含了图像分析导出的结果文件，涵盖了用于捕获每个单个细胞形态特征的单对象测量数据。每个文件夹对应一块微孔板的测量结果，代表一次独立的生物学重复。这些数据为图像分析的原始输出文件，尚未经过标准化处理或筛选剔除。 文件Compound_layout.xlsx 提供了微孔板布局的详细信息，包括已测试的化合物及其工作浓度。文件Table_to_exclude_wells.xlsx 列出了因移液错误等技术问题，需在下游分析中剔除的孔位。每块微孔板每孔成像5个视野，并采集两个光学切片（z平面）；每块微孔板的分析用z平面信息详见Table_planes.xlsx。 本数据集可作为CPPAnalyzer Jupyter笔记本（可于Wedler等人2026年的研究中获取，https://doi.org/10.5281/zenodo.18385218）的输入文件，用于对数据进行归一化与标准化处理，以支持后续分析。 数据集normalized_data.zip 包含了使用CPPAnalyzer Jupyter笔记本并按照251219_U2OS.ipynb中的设置完成标准化处理的数据。经标准化处理的数据可作为CPPManager KNIME工作流（可于Wedler等人2026年的研究中获取，https://doi.org/10.5281/zenodo.18385218）的输入文件。 文件Fig1、Fig2与Fig3 包含了用于生成Wedler等人（2026年）论文《细胞绘画PLUS：高内涵表型筛选的迭代染色-洗脱方案》（《Current Protocols》，DOI:10.1002/cpz1.70368）中各图表的源数据。