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Related Experiment Video

Updated: Jun 9, 2026

Laser-Capture Microdissection RNA-Sequencing for Spatial and Temporal Tissue-Specific Gene Expression Analysis in Plants

Laser-Capture Microdissection RNA-Sequencing for Spatial and Temporal Tissue-Specific Gene Expression Analysis in Plants

Published on: August 5, 2020

Quantitative RNA spatial profiling using single-molecule RNA FISH on plant tissue cryosections.

Xue Zhang¹, Alejandro Fonseca¹, Konstantin Kutashev¹

¹Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.

Plant Communications

|June 8, 2026

Summary

This summary is machine-generated.

We developed cryo-smFISH, a simple and robust method for visualizing single mRNA molecules in plant tissue sections. This technique accurately quantifies gene expression in cellular compartments and validates single-cell RNA sequencing data.

Keywords:

quantitative gene expression scRNA-seq smFISH smFISH-IF tissue cryosections

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Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

Area of Science:

Molecular Biology
Plant Science
Genetics

Background:

Single-molecule fluorescence in situ hybridization (smFISH) is crucial for studying gene expression dynamics.
Existing smFISH methods require adaptation for plant tissue sections.

Purpose of the Study:

To present an optimized smFISH protocol (cryo-smFISH) for plant tissue cryosections.
To enable sensitive detection and quantification of RNA molecules in plant cells.

Main Methods:

Developed cryo-smFISH protocol for plant tissue cryosections.
Integrated a deep learning algorithm for RNA abundance analysis in nuclear and cytoplasmic compartments.
Combined smFISH with immunofluorescence for simultaneous RNA and protein visualization.

Main Results:

Cryo-smFISH demonstrates high sensitivity, detecting low-expression transcripts like long non-coding RNAs.
The method allows precise RNA quantification within distinct cellular compartments.
Cryosectioning improved antibody penetration, enabling robust RNA-protein co-visualization.
Validated single-cell RNA sequencing (scRNA-seq) expression patterns in plant tissues.

Conclusions:

Cryo-smFISH offers a robust and sensitive method for analyzing gene expression in plant tissues.
This protocol facilitates quantitative transcript analysis at cellular and subcellular resolutions.
The method enhances the utility of smFISH for a broader plant science community.