September 8, 2026 Dataset Open Access

VACV LC3 lipidation Screen Dataset

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

This repository contains the analysis pipeline, quantitative cytometry measurements, and experimental plate layouts associated with the study:

Granularity screening identifies candidate genes involved in vaccinia virus induced LC3 lipidation
Melanie Krause, Artur Yakimovich, Noemi Vágó, Ingo Drexler, Jason Mercer
bioRxiv (2026)
DOI: 10.64898/2026.03.26.714436

Overview

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 LC3 granularity as a quantitative imaging phenotype.

This deposition contains:

• the image-analysis pipeline used for the screening;

• quantitative single-cell measurements generated from the screening plates; and

• the corresponding experimental plate layouts.

The data are provided to facilitate reproducibility and reuse of the quantitative screening results reported in the associated preprint.

Contents

File | Size | Description

LC3_screen_pipeline.cpproj | 1.8 MB  | Image-analysis pipeline/project used to process the LC3 screening data.

plate1_full_cyt.csv| 15.1 MB | Quantitative single-cell cytometry measurements for screening plate 1.

plate2_full_cyt.csv| 17.6 MB | Quantitative single-cell cytometry measurements for screening plate 2.

plate3_full_cyt.csv| 18.2 MB | Quantitative single-cell cytometry measurements for screening plate 3.

plate4_full_cyt.csv| 15.9 MB | Quantitative single-cell cytometry measurements for screening plate 4.

plate5_full_cyt.csv| 17.2 MB | Quantitative single-cell cytometry measurements for screening plate 5.

plate6_full_cyt.csv| 17.9 MB | Quantitative single-cell cytometry measurements for screening plate 6.

Screening_Plate_Layout_1_1-40.xlsx | 9 KB  | Experimental layout for screening plate 1.

Screening_Plate_Layout_2_2-40.xlsx | 9 KB | Experimental layout for screening plate 2.

Screening_Plate_Layout_3_3-40.xlsx | 9 KB | Experimental layout for screening plate 3.

Screening_Plate_Layout_4_1-40.xlsx | 9 KB | Experimental layout for screening plate 4.

Screening_Plate_Layout_5_2-40.xlsx | 9 KB | Experimental layout for screening plate 5.

Screening_Plate_Layout_6_3-40.xlsx | 9 KB | Experimental layout for screening plate 6.

File descriptions

Image-analysis pipeline

LC3_screen_pipeline.cpproj

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.

Quantitative measurements

The files

• plate1_full_cyt.csv

• plate2_full_cyt.csv

• plate3_full_cyt.csv

• plate4_full_cyt.csv

• plate5_full_cyt.csv

• plate6_full_cyt.csv

contain the quantitative measurements generated for individual cells from the six screening plates.

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.

The measurements are provided in tabular CSV format to facilitate analysis using standard data-analysis tools such as Python, R, MATLAB, or spreadsheet software.

Screening plate layouts

The six Excel files contain the corresponding experimental layouts for the screening plates:

• Screening_Plate_Layout_1_1-40.xlsx

• Screening_Plate_Layout_2_2-40.xlsx

• Screening_Plate_Layout_3_3-40.xlsx

• Screening_Plate_Layout_4_1-40.xlsx

• Screening_Plate_Layout_5_2-40.xlsx

• Screening_Plate_Layout_6_3-40.xlsx

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.

Relationship between files

The deposited files can be considered in three complementary layers:

1. Plate layouts (.xlsx)
   Define the experimental organization and contents of each screening plate.

2. Image-analysis pipeline (.cpproj)
   Documents the image-processing and quantitative measurement workflow.

3. Quantitative measurements (.csv)
   Contain the resulting single-cell measurements for each screening plate.

Together, these files provide the experimental metadata, analysis workflow, and quantitative output required to reproduce or further analyze the screening results.

Data organization

Each screening plate has one corresponding quantitative measurement file:

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

The corresponding Excel plate-layout files provide the experimental context for each plate.

'LC3_Screen_Information.xlsx' contain VACV gene keys.

Intended use

The deposited data may be used to:

• reproduce the quantitative analyses reported in the associated study;

• inspect the distribution of single-cell LC3-related measurements;

• perform alternative or extended analyses of the screening data;

• develop or benchmark computational methods for quantitative image-based screening; and

• investigate candidate VACV genes associated with changes in LC3 granularity.

Citation

If you use these data, please cite the associated preprint:

Krause M, Yakimovich A, Vágó N, Drexler I, Mercer J.
Granularity screening identifies candidate genes involved in vaccinia virus induced LC3 lipidation.
bioRxiv, 2026.
https://doi.org/10.64898/2026.03.26.714436

Data provenance

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.

For methodological details, experimental procedures, and interpretation of the screening results, please refer to the associated publication.

Contact

For questions regarding the dataset or analysis pipeline, please contact the corresponding authors of the associated study.