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bioRxiv · 10.1101/2024.11.14.623566

autoFISH - a modular toolbox for sequential smFISH experiments

Weber, C.·Defard, T.·Lelek, M.·Laporte, H.·Mallick, A.·Londono-Vallejo, J.-A.·Walter, T.·Fouillade, C.·Gariboldi, M. I.·Muller, F.
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Abstract

Fluorescence in situ hybridization (FISH) allows for spatial and quantitative profiling of gene expression by visualizing individual RNA molecules. Here, we introduce automated FISH (autoFISH), a comprehensive toolbox to conduct automated single molecule FISH (smFISH) experiments that is both cost-effective and versatile. This includes detailed plans for constructing the necessary equipment, open-source software for control, reliable experimental protocols, and analysis workflows based on our FISH-quant analysis package. Validation experiments with both cell lines and tissue samples confirmed the systems robustness. We demonstrate standard and amplified smFISH, along with a modified protocol for tissue clearing that enhances nuclear retention while preserving background reduction efficiency.

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Weber, C., Defard, T., Lelek, M., Laporte, H., Mallick, A., Londono-Vallejo, J.-A., Walter, T., Fouillade, C., Gariboldi, M. I., Muller, F.. 2024-11-15. autoFISH - a modular toolbox for sequential smFISH experiments. https://doi.org/10.1101/2024.11.14.623566

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