Sample Preparation for Imaging-Based Spatial Transcriptomics in Rigid Plant Tissues (Roots, Shoots)

Area of Science:

• Plant Biology
• Molecular Biology
• Genomics

Background:

• Plant roots are crucial for development and gene regulation, responding dynamically to environmental stimuli.
• Imaging-based spatial transcriptomics offers high-resolution gene expression mapping with spatial context.
• Current methods struggle with preparing rigid plant tissues for spatial transcriptomics.

Purpose of the Study:

• To present a practical protocol for preparing rigid plant tissue samples for imaging-based spatial transcriptomics.
• To optimize sample preparation for effective tissue handling, RNA integrity, and spatial organization.
• To enable broader application of spatial transcriptomics in plant research.

Main Methods:

• Developed a detailed protocol building upon existing methods for rigid plant tissue preparation.
• Incorporated steps for effective tissue fixation, sectioning, and RNA preservation.
• Included an integrated sample attachment test to evaluate tissue adhesion to slides.

Main Results:

• The protocol successfully prepares rigid plant tissues, such as rice roots, for spatial transcriptomics.
• RNA integrity and spatial organization are maintained throughout the sample preparation process.
• The integrated attachment test ensures reliable sample adhesion to commercial slides.

Conclusions:

• This optimized protocol provides a robust solution for spatial transcriptomic analysis in rigid plant tissues.
• The 8-day workflow facilitates consistent and reliable gene expression mapping in plants.
• Enables advanced research into plant cell development and gene regulation using spatial transcriptomics.