September 8, 2026 Dataset Open Access

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

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      "Granularity screening identifies candidate genes involved in vaccinia virus induced LC3 lipidation Melanie Krause, Artur Yakimovich, Noemi V\u00e1g\u00f3, Ingo Drexler, Jason Mercer bioRxiv (2026) DOI: 10.64898/2026.03.26.714436"
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    "title": "VACV LC3 lipidation Screen Dataset", 
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    "description": "<p>This repository contains the analysis pipeline, quantitative cytometry measurements, and experimental plate layouts associated with the study:</p>\n\n<blockquote>\n<p><strong>Granularity screening identifies candidate genes involved in vaccinia virus induced LC3 lipidation</strong><br>\nMelanie Krause, Artur Yakimovich, Noemi V&aacute;g&oacute;, Ingo Drexler, Jason Mercer<br>\nbioRxiv (2026)<br>\nDOI: <a href=\"https://doi.org/10.64898/2026.03.26.714436\">10.64898/2026.03.26.714436</a></p>\n</blockquote>\n\n\n\n<p><strong>Overview</strong></p>\n\n<p>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 <strong>LC3 granularity</strong> as a quantitative imaging phenotype.</p>\n\n<p>This deposition contains:</p>\n\n<ul>\n\t<li>\n\t<p>the image-analysis pipeline used for the screening;</p>\n\t</li>\n\t<li>\n\t<p>quantitative single-cell measurements generated from the screening plates; and</p>\n\t</li>\n\t<li>\n\t<p>the corresponding experimental plate layouts.</p>\n\t</li>\n</ul>\n\n<p>The data are provided to facilitate reproducibility and reuse of the quantitative screening results reported in the associated preprint.</p>\n\n\n\n<p><strong>Contents</strong></p>\n\n<p><em>File | Size | Description</em></p>\n\n<p><code>LC3_screen_pipeline.cpproj |&nbsp;</code>1.8 MB&nbsp; | Image-analysis pipeline/project used to process the LC3 screening data.</p>\n\n<p><code>plate1_full_cyt.csv|&nbsp;</code>15.1 MB&nbsp;<code>|&nbsp;</code>Quantitative single-cell cytometry measurements for screening plate 1.</p>\n\n<p><code>plate2_full_cyt.csv|&nbsp;</code>17.6 MB&nbsp;<code>|&nbsp;</code>Quantitative single-cell cytometry measurements for screening plate 2.</p>\n\n<p><code>plate3_full_cyt.csv|&nbsp;</code>18.2 MB&nbsp;<code>|&nbsp;</code>Quantitative single-cell cytometry measurements for screening plate 3.</p>\n\n<p><code>plate4_full_cyt.csv|&nbsp;</code>15.9 MB&nbsp;<code>|&nbsp;</code>Quantitative single-cell cytometry measurements for screening plate 4.</p>\n\n<p><code>plate5_full_cyt.csv|&nbsp;</code>17.2 MB&nbsp;<code>|&nbsp;</code>Quantitative single-cell cytometry measurements for screening plate 5.</p>\n\n<p><code>plate6_full_cyt.csv|&nbsp;</code>17.9 MB&nbsp;<code>|&nbsp;</code>Quantitative single-cell cytometry measurements for screening plate 6.</p>\n\n<p><code>Screening_Plate_Layout_1_1-40.xlsx |&nbsp;</code>9 KB&nbsp; | Experimental layout for screening plate 1.</p>\n\n<p><code>Screening_Plate_Layout_2_2-40.xlsx |&nbsp;</code>9 KB&nbsp;<code>|&nbsp;</code>Experimental layout for screening plate 2.</p>\n\n<p><code>Screening_Plate_Layout_3_3-40.xlsx |&nbsp;</code>9 KB&nbsp;<code>|&nbsp;</code>Experimental layout for screening plate 3.</p>\n\n<p><code>Screening_Plate_Layout_4_1-40.xlsx |&nbsp;</code>9 KB <code>|&nbsp;</code>Experimental layout for screening plate 4.</p>\n\n<p><code>Screening_Plate_Layout_5_2-40.xlsx |&nbsp;</code>9 KB <code>|&nbsp;</code>Experimental layout for screening plate 5.</p>\n\n<p><code>Screening_Plate_Layout_6_3-40.xlsx |&nbsp;</code>9 KB&nbsp;<code>|&nbsp;</code>Experimental layout for screening plate 6.</p>\n\n\n\n<p><strong>File descriptions</strong></p>\n\n<p>Image-analysis pipeline</p>\n\n<p><code>LC3_screen_pipeline.cpproj</code></p>\n\n<p>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.</p>\n\n<p><em>Quantitative measurements</em></p>\n\n<p>The files</p>\n\n<ul>\n\t<li>\n\t<p><code>plate1_full_cyt.csv</code></p>\n\t</li>\n\t<li>\n\t<p><code>plate2_full_cyt.csv</code></p>\n\t</li>\n\t<li>\n\t<p><code>plate3_full_cyt.csv</code></p>\n\t</li>\n\t<li>\n\t<p><code>plate4_full_cyt.csv</code></p>\n\t</li>\n\t<li>\n\t<p><code>plate5_full_cyt.csv</code></p>\n\t</li>\n\t<li>\n\t<p><code>plate6_full_cyt.csv</code></p>\n\t</li>\n</ul>\n\n<p>contain the quantitative measurements generated for individual cells from the six screening plates.</p>\n\n<p>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.</p>\n\n<p>The measurements are provided in tabular CSV format to facilitate analysis using standard data-analysis tools such as Python, R, MATLAB, or spreadsheet software.</p>\n\n<p><em>Screening plate layouts</em></p>\n\n<p>The six Excel files contain the corresponding experimental layouts for the screening plates:</p>\n\n<ul>\n\t<li>\n\t<p><code>Screening_Plate_Layout_1_1-40.xlsx</code></p>\n\t</li>\n\t<li>\n\t<p><code>Screening_Plate_Layout_2_2-40.xlsx</code></p>\n\t</li>\n\t<li>\n\t<p><code>Screening_Plate_Layout_3_3-40.xlsx</code></p>\n\t</li>\n\t<li>\n\t<p><code>Screening_Plate_Layout_4_1-40.xlsx</code></p>\n\t</li>\n\t<li>\n\t<p><code>Screening_Plate_Layout_5_2-40.xlsx</code></p>\n\t</li>\n\t<li>\n\t<p><code>Screening_Plate_Layout_6_3-40.xlsx</code></p>\n\t</li>\n</ul>\n\n<p>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.</p>\n\n\n\n<p><strong>Relationship between files</strong></p>\n\n<p>The deposited files can be considered in three complementary layers:</p>\n\n<ol>\n\t<li>\n\t<p><strong>Plate layouts (<code>.xlsx</code>)</strong><br>\n\tDefine the experimental organization and contents of each screening plate.</p>\n\t</li>\n\t<li>\n\t<p><strong>Image-analysis pipeline (<code>.cpproj</code>)</strong><br>\n\tDocuments the image-processing and quantitative measurement workflow.</p>\n\t</li>\n\t<li>\n\t<p><strong>Quantitative measurements (<code>.csv</code>)</strong><br>\n\tContain the resulting single-cell measurements for each screening plate.</p>\n\t</li>\n</ol>\n\n<p>Together, these files provide the experimental metadata, analysis workflow, and quantitative output required to reproduce or further analyze the screening results.</p>\n\n<p>Data organization</p>\n\n<p>Each screening plate has one corresponding quantitative measurement file:</p>\n\n<pre><code>Plate 1 \u2192 plate1_full_cyt.csv\nPlate 2 \u2192 plate2_full_cyt.csv\nPlate 3 \u2192 plate3_full_cyt.csv\nPlate 4 \u2192 plate4_full_cyt.csv\nPlate 5 \u2192 plate5_full_cyt.csv\nPlate 6 \u2192 plate6_full_cyt.csv\n</code></pre>\n\n<p>The corresponding Excel plate-layout files provide the experimental context for each plate.</p>\n\n\n\n<p>&#39;LC3_Screen_Information.xlsx&#39; contain VACV gene keys.</p>\n\n<p><strong>Intended use</strong></p>\n\n<p>The deposited data may be used to:</p>\n\n<ul>\n\t<li>\n\t<p>reproduce the quantitative analyses reported in the associated study;</p>\n\t</li>\n\t<li>\n\t<p>inspect the distribution of single-cell LC3-related measurements;</p>\n\t</li>\n\t<li>\n\t<p>perform alternative or extended analyses of the screening data;</p>\n\t</li>\n\t<li>\n\t<p>develop or benchmark computational methods for quantitative image-based screening; and</p>\n\t</li>\n\t<li>\n\t<p>investigate candidate VACV genes associated with changes in LC3 granularity.</p>\n\t</li>\n</ul>\n\n\n\n<p><strong>Citation</strong></p>\n\n<p>If you use these data, please cite the associated preprint:</p>\n\n<p><strong>Krause M, Yakimovich A, V&aacute;g&oacute; N, Drexler I, Mercer J.</strong><br>\n<em>Granularity screening identifies candidate genes involved in vaccinia virus induced LC3 lipidation.</em><br>\nbioRxiv, 2026.<br>\n<a href=\"https://doi.org/10.64898/2026.03.26.714436\">https://doi.org/10.64898/2026.03.26.714436</a></p>\n\n\n\n<p><strong>Data provenance</strong></p>\n\n<p>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.</p>\n\n<p>For methodological details, experimental procedures, and interpretation of the screening results, please refer to the associated publication.</p>\n\n\n\n<p><strong>Contact</strong></p>\n\n<p>For questions regarding the dataset or analysis pipeline, please contact the corresponding authors of the associated study.</p>", 
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