autoFISH: a modular toolbox for sequential single-molecule RNA FISH experiments

Area of Science:

• Molecular Biology
• Genomics
• Biotechnology

Background:

• Spatial and quantitative detection of RNA molecules is crucial for understanding gene expression, cellular function, and tissue organization.
• Widespread adoption of automated single-molecule fluorescence in situ hybridization (smFISH) is hindered by high equipment costs and experimental complexity.

Purpose of the Study:

• To present autoFISH, an affordable and user-friendly platform designed to overcome the barriers associated with automated smFISH.
• To enable broader accessibility to spatial transcriptomics research through simplified procedures and reduced costs.

Main Methods:

• Development of an open-source hardware platform with accessible control software and integrated analysis tools.
• Implementation of both conventional and signal-amplified smFISH protocols.
• Incorporation of an optimized tissue-clearing method to preserve nuclear structures.

Main Results:

• The autoFISH system demonstrates broad applicability across multiple cell types and tissue preparations.
• Validation of the system's reliability and reproducibility in spatial transcriptomics experiments.
• Significant reduction in costs and technical expertise required for smFISH.

Conclusions:

• autoFISH offers a practical solution for scaling spatial transcriptomics research.
• The platform facilitates advancements in cellular and developmental biology by democratizing access to single-molecule detection techniques.
• This innovation lowers the barrier to entry for researchers interested in gene expression analysis at the single-molecule level.