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Article Dans Une Revue RNA Année : 2022

FISH-quant v2: a scalable and modular tool for smFISH image analysis

Résumé

Regulation of RNA abundance and localization is a key step in gene expression control. Single-molecule RNA fluorescence in situ hybridization (smFISH) is a widely used single-cell-single-molecule imaging technique enabling quantitative studies of gene expression and its regulatory mechanisms. Today, these methods are applicable at a large scale, which in turn come with a need for adequate tools for data analysis and exploration. Here, we present FISH-quant v2, a highly modular tool accessible for both experts and non-experts. Our user-friendly package allows the user to segment nuclei and cells, detect isolated RNAs, decompose dense RNA clusters, quantify RNA localization patterns and visualize these results both at the single-cell level and variations within the cell population. This tool was validated and applied on large-scale smFISH image data sets, revealing diverse subcellular RNA localization patterns and a surprisingly high degree of cell-to-cell heterogeneity.
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Licence : CC BY NC - Paternité - Pas d'utilisation commerciale

Dates et versions

hal-03942851 , version 1 (18-01-2022)
hal-03942851 , version 2 (17-01-2023)

Licence

Paternité - Pas d'utilisation commerciale

Identifiants

Citer

Arthur Imbert, Wei Ouyang, Adham Safieddine, Emeline Coleno, Christophe Zimmer, et al.. FISH-quant v2: a scalable and modular tool for smFISH image analysis. RNA, 2022, 28 (6), pp.786-795. ⟨10.1261/rna.079073.121⟩. ⟨hal-03942851v2⟩
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