ArticlePlant methods2023
A rapid and sensitive, multiplex, whole mount RNA fluorescence in situ hybridization and immunohistochemistry protocol.
Article in Plant methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 24 citations in OpenAlex.
- Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward.The Plant cell · 2026Review
- ARABIDOPSIS Bsister and SEEDSTICK MADS-box transcription factors modulate maternal nutrient flow for seed development in Arabidopsis.Nature communications · 2026Article
- Quantitative RNA spatial profiling using single-molecule RNA FISH on plant tissue cryosections.Plant communications · 2026Article
- Single-nucleus transcriptomics resolves multiple fate dynamics between inflorescence meristem and primary stem.Science advances · 2026Article
- The developing leaf of the wild grass Brachypodium distachyon at single-cell resolution.The Plant cell · 2026Article
- Review
- A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination.Nature plants · 2026Article
- Optimizing the hybridization chain reaction-fluorescence in situ hybridization (HCR-FISH) protocol forbioRxiv : the preprint server for biology · 2026Article
- Modern RNA Quantification Methods: From RT-qPCR to Advanced Microscopy.The journal of physical chemistry. B · 2026Review
- smoppix: unified nonparametric analysis of single-molecule spatial omics data using probabilistic indices.Genome biology · 2026Article
- Evolutionary adaptations to the hormonal regulation of vascular tissue development.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Why "Where" Matters as Much as "How Much": Single-Cell and Spatial Transcriptomics in Plants.International journal of molecular sciences · 2025Review
- Long Noncoding RNAs as Emerging Regulators of Seed Development, Germination, and Senescence.International journal of molecular sciences · 2025Review
- Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics.The New phytologist · 2025Article
- Glutathione accelerates the cell cycle and cellular reprogramming in plant regeneration.Developmental cell · 2025Article
- Moisture-responsive root-branching pathways identified in diverse maize breeding germplasm.Science (New York, N.Y.) · 2025Article
- Dual role of BdMUTE during stomatal development in the model grass Brachypodium distachyon.Development (Cambridge, England) · 2024Article
- Glutathione accelerates the cell cycle and cellular reprogramming in plant regeneration.bioRxiv : the preprint server for biology · 2024Article
- A common regulatory switch controls a suite of C4 traits in multiple cell types.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundIn the past few years, there has been an explosion in single-cell transcriptomics datasets, yet in vivo confirmation of these datasets is hampered in plants due to lack of robust validation methods. Likewise, modeling of plant development is hampered by paucity of spatial gene expression data. RNA fluorescence in situ hybridization (FISH) enables investigation of gene expression in the context of tissue type. Despite development of FISH methods for plants, easy and reliable whole mount FISH protocols have not yet been reported.
resultsWe adapt a 3-day whole mount RNA-FISH method for plant species based on a combination of prior protocols that employs hybridization chain reaction (HCR), which amplifies the probe signal in an antibody-free manner. Our whole mount HCR RNA-FISH method shows expected spatial signals with low background for gene transcripts with known spatial expression patterns in Arabidopsis inflorescences and monocot roots. It allows simultaneous detection of three transcripts in 3D. We also show that HCR RNA-FISH can be combined with endogenous fluorescent protein detection and with our improved immunohistochemistry (IHC) protocol.
conclusionsThe whole mount HCR RNA-FISH and IHC methods allow easy investigation of 3D spatial gene expression patterns in entire plant tissues.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.