September 8, 2026 Dataset Open Access

Krause, Melanie; Yakimovich, Artur; Vágó, Noemi; Drexler, Ingo; Mercer, Jason

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    <dct:title>VACV LC3 lipidation Screen Dataset</dct:title>
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    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2026</dct:issued>
    <dcat:keyword>vaccinia virus</dcat:keyword>
    <dcat:keyword>high-content screening</dcat:keyword>
    <dcat:keyword>autophagy</dcat:keyword>
    <dcat:keyword>granularity</dcat:keyword>
    <dcat:keyword>single-cell analysis</dcat:keyword>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2026-09-08</dct:issued>
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    <dct:description>&lt;p&gt;This repository contains the analysis pipeline, quantitative cytometry measurements, and experimental plate layouts associated with the study:&lt;/p&gt; &lt;blockquote&gt; &lt;p&gt;&lt;strong&gt;Granularity screening identifies candidate genes involved in vaccinia virus induced LC3 lipidation&lt;/strong&gt;&lt;br&gt; Melanie Krause, Artur Yakimovich, Noemi V&amp;aacute;g&amp;oacute;, Ingo Drexler, Jason Mercer&lt;br&gt; bioRxiv (2026)&lt;br&gt; DOI: &lt;a href="https://doi.org/10.64898/2026.03.26.714436"&gt;10.64898/2026.03.26.714436&lt;/a&gt;&lt;/p&gt; &lt;/blockquote&gt; &lt;p&gt;&lt;strong&gt;Overview&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;The deposited data were generated as part of an image-based screening approach designed to identify candidate vaccinia virus (VACV) genes that affect LC3 lipidation. The screening uses &lt;strong&gt;LC3 granularity&lt;/strong&gt; as a quantitative imaging phenotype.&lt;/p&gt; &lt;p&gt;This deposition contains:&lt;/p&gt; &lt;ul&gt; &lt;li&gt; &lt;p&gt;the image-analysis pipeline used for the screening;&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;quantitative single-cell measurements generated from the screening plates; and&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;the corresponding experimental plate layouts.&lt;/p&gt; &lt;/li&gt; &lt;/ul&gt; &lt;p&gt;The data are provided to facilitate reproducibility and reuse of the quantitative screening results reported in the associated preprint.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Contents&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;&lt;em&gt;File | Size | Description&lt;/em&gt;&lt;/p&gt; &lt;p&gt;&lt;code&gt;LC3_screen_pipeline.cpproj |&amp;nbsp;&lt;/code&gt;1.8 MB&amp;nbsp; | Image-analysis pipeline/project used to process the LC3 screening data.&lt;/p&gt; &lt;p&gt;&lt;code&gt;plate1_full_cyt.csv|&amp;nbsp;&lt;/code&gt;15.1 MB&amp;nbsp;&lt;code&gt;|&amp;nbsp;&lt;/code&gt;Quantitative single-cell cytometry measurements for screening plate 1.&lt;/p&gt; &lt;p&gt;&lt;code&gt;plate2_full_cyt.csv|&amp;nbsp;&lt;/code&gt;17.6 MB&amp;nbsp;&lt;code&gt;|&amp;nbsp;&lt;/code&gt;Quantitative single-cell cytometry measurements for screening plate 2.&lt;/p&gt; &lt;p&gt;&lt;code&gt;plate3_full_cyt.csv|&amp;nbsp;&lt;/code&gt;18.2 MB&amp;nbsp;&lt;code&gt;|&amp;nbsp;&lt;/code&gt;Quantitative single-cell cytometry measurements for screening plate 3.&lt;/p&gt; &lt;p&gt;&lt;code&gt;plate4_full_cyt.csv|&amp;nbsp;&lt;/code&gt;15.9 MB&amp;nbsp;&lt;code&gt;|&amp;nbsp;&lt;/code&gt;Quantitative single-cell cytometry measurements for screening plate 4.&lt;/p&gt; &lt;p&gt;&lt;code&gt;plate5_full_cyt.csv|&amp;nbsp;&lt;/code&gt;17.2 MB&amp;nbsp;&lt;code&gt;|&amp;nbsp;&lt;/code&gt;Quantitative single-cell cytometry measurements for screening plate 5.&lt;/p&gt; &lt;p&gt;&lt;code&gt;plate6_full_cyt.csv|&amp;nbsp;&lt;/code&gt;17.9 MB&amp;nbsp;&lt;code&gt;|&amp;nbsp;&lt;/code&gt;Quantitative single-cell cytometry measurements for screening plate 6.&lt;/p&gt; &lt;p&gt;&lt;code&gt;Screening_Plate_Layout_1_1-40.xlsx |&amp;nbsp;&lt;/code&gt;9 KB&amp;nbsp; | Experimental layout for screening plate 1.&lt;/p&gt; &lt;p&gt;&lt;code&gt;Screening_Plate_Layout_2_2-40.xlsx |&amp;nbsp;&lt;/code&gt;9 KB&amp;nbsp;&lt;code&gt;|&amp;nbsp;&lt;/code&gt;Experimental layout for screening plate 2.&lt;/p&gt; &lt;p&gt;&lt;code&gt;Screening_Plate_Layout_3_3-40.xlsx |&amp;nbsp;&lt;/code&gt;9 KB&amp;nbsp;&lt;code&gt;|&amp;nbsp;&lt;/code&gt;Experimental layout for screening plate 3.&lt;/p&gt; &lt;p&gt;&lt;code&gt;Screening_Plate_Layout_4_1-40.xlsx |&amp;nbsp;&lt;/code&gt;9 KB &lt;code&gt;|&amp;nbsp;&lt;/code&gt;Experimental layout for screening plate 4.&lt;/p&gt; &lt;p&gt;&lt;code&gt;Screening_Plate_Layout_5_2-40.xlsx |&amp;nbsp;&lt;/code&gt;9 KB &lt;code&gt;|&amp;nbsp;&lt;/code&gt;Experimental layout for screening plate 5.&lt;/p&gt; &lt;p&gt;&lt;code&gt;Screening_Plate_Layout_6_3-40.xlsx |&amp;nbsp;&lt;/code&gt;9 KB&amp;nbsp;&lt;code&gt;|&amp;nbsp;&lt;/code&gt;Experimental layout for screening plate 6.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;File descriptions&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Image-analysis pipeline&lt;/p&gt; &lt;p&gt;&lt;code&gt;LC3_screen_pipeline.cpproj&lt;/code&gt;&lt;/p&gt; &lt;p&gt;This file contains the CellProfiler image-analysis project used to process the screening images and extract quantitative cellular measurements. The project is provided to document the image-processing and measurement workflow used to generate the deposited quantitative data.&lt;/p&gt; &lt;p&gt;&lt;em&gt;Quantitative measurements&lt;/em&gt;&lt;/p&gt; &lt;p&gt;The files&lt;/p&gt; &lt;ul&gt; &lt;li&gt; &lt;p&gt;&lt;code&gt;plate1_full_cyt.csv&lt;/code&gt;&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;&lt;code&gt;plate2_full_cyt.csv&lt;/code&gt;&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;&lt;code&gt;plate3_full_cyt.csv&lt;/code&gt;&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;&lt;code&gt;plate4_full_cyt.csv&lt;/code&gt;&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;&lt;code&gt;plate5_full_cyt.csv&lt;/code&gt;&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;&lt;code&gt;plate6_full_cyt.csv&lt;/code&gt;&lt;/p&gt; &lt;/li&gt; &lt;/ul&gt; &lt;p&gt;contain the quantitative measurements generated for individual cells from the six screening plates.&lt;/p&gt; &lt;p&gt;The CSV files are intended to provide the underlying single-cell measurements used for downstream analysis of the LC3 granularity phenotype. Each file corresponds to one screening plate.&lt;/p&gt; &lt;p&gt;The measurements are provided in tabular CSV format to facilitate analysis using standard data-analysis tools such as Python, R, MATLAB, or spreadsheet software.&lt;/p&gt; &lt;p&gt;&lt;em&gt;Screening plate layouts&lt;/em&gt;&lt;/p&gt; &lt;p&gt;The six Excel files contain the corresponding experimental layouts for the screening plates:&lt;/p&gt; &lt;ul&gt; &lt;li&gt; &lt;p&gt;&lt;code&gt;Screening_Plate_Layout_1_1-40.xlsx&lt;/code&gt;&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;&lt;code&gt;Screening_Plate_Layout_2_2-40.xlsx&lt;/code&gt;&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;&lt;code&gt;Screening_Plate_Layout_3_3-40.xlsx&lt;/code&gt;&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;&lt;code&gt;Screening_Plate_Layout_4_1-40.xlsx&lt;/code&gt;&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;&lt;code&gt;Screening_Plate_Layout_5_2-40.xlsx&lt;/code&gt;&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;&lt;code&gt;Screening_Plate_Layout_6_3-40.xlsx&lt;/code&gt;&lt;/p&gt; &lt;/li&gt; &lt;/ul&gt; &lt;p&gt;These files provide the mapping between experimental conditions and positions on the respective screening plates and should be used together with the corresponding quantitative measurement files.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Relationship between files&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;The deposited files can be considered in three complementary layers:&lt;/p&gt; &lt;ol&gt; &lt;li&gt; &lt;p&gt;&lt;strong&gt;Plate layouts (&lt;code&gt;.xlsx&lt;/code&gt;)&lt;/strong&gt;&lt;br&gt; Define the experimental organization and contents of each screening plate.&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;&lt;strong&gt;Image-analysis pipeline (&lt;code&gt;.cpproj&lt;/code&gt;)&lt;/strong&gt;&lt;br&gt; Documents the image-processing and quantitative measurement workflow.&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;&lt;strong&gt;Quantitative measurements (&lt;code&gt;.csv&lt;/code&gt;)&lt;/strong&gt;&lt;br&gt; Contain the resulting single-cell measurements for each screening plate.&lt;/p&gt; &lt;/li&gt; &lt;/ol&gt; &lt;p&gt;Together, these files provide the experimental metadata, analysis workflow, and quantitative output required to reproduce or further analyze the screening results.&lt;/p&gt; &lt;p&gt;Data organization&lt;/p&gt; &lt;p&gt;Each screening plate has one corresponding quantitative measurement file:&lt;/p&gt; &lt;pre&gt;&lt;code&gt;Plate 1 → plate1_full_cyt.csv Plate 2 → plate2_full_cyt.csv Plate 3 → plate3_full_cyt.csv Plate 4 → plate4_full_cyt.csv Plate 5 → plate5_full_cyt.csv Plate 6 → plate6_full_cyt.csv &lt;/code&gt;&lt;/pre&gt; &lt;p&gt;The corresponding Excel plate-layout files provide the experimental context for each plate.&lt;/p&gt; &lt;p&gt;&amp;#39;LC3_Screen_Information.xlsx&amp;#39; contain VACV gene keys.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Intended use&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;The deposited data may be used to:&lt;/p&gt; &lt;ul&gt; &lt;li&gt; &lt;p&gt;reproduce the quantitative analyses reported in the associated study;&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;inspect the distribution of single-cell LC3-related measurements;&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;perform alternative or extended analyses of the screening data;&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;develop or benchmark computational methods for quantitative image-based screening; and&lt;/p&gt; &lt;/li&gt; &lt;li&gt; &lt;p&gt;investigate candidate VACV genes associated with changes in LC3 granularity.&lt;/p&gt; &lt;/li&gt; &lt;/ul&gt; &lt;p&gt;&lt;strong&gt;Citation&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;If you use these data, please cite the associated preprint:&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Krause M, Yakimovich A, V&amp;aacute;g&amp;oacute; N, Drexler I, Mercer J.&lt;/strong&gt;&lt;br&gt; &lt;em&gt;Granularity screening identifies candidate genes involved in vaccinia virus induced LC3 lipidation.&lt;/em&gt;&lt;br&gt; bioRxiv, 2026.&lt;br&gt; &lt;a href="https://doi.org/10.64898/2026.03.26.714436"&gt;https://doi.org/10.64898/2026.03.26.714436&lt;/a&gt;&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Data provenance&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;These data were generated as part of the experiments described in the associated preprint. The deposition contains the analysis project, quantitative measurements, and experimental plate layouts used in the study.&lt;/p&gt; &lt;p&gt;For methodological details, experimental procedures, and interpretation of the screening results, please refer to the associated publication.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Contact&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;For questions regarding the dataset or analysis pipeline, please contact the corresponding authors of the associated study.&lt;/p&gt;</dct:description>
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