ArticleNature protocols2018
Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays.
Article in Nature protocols, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
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Who cites it
31 citing papers in PubMed, 57 citations in OpenAlex.
- Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward.The Plant cell · 2026Review
- Spatial transcriptome analysis of the tea tender shoot sheds light on transcriptional regulation of characteristic metabolites.Horticulture research · 2026Article
- Deciphering skeletal muscle development: cellular heterogeneity and molecular regulatory networks from single-cell and spatial transcriptomic perspectives.Frontiers in cell and developmental biology · 2026Review
- Single-cell omics in plant biology: mechanistic insights and applications for crop improvement.Advanced biotechnology · 2025Review
- GhLPF1 Associated Network Is Involved with Cotton Lint Percentage Regulation Revealed by the Integrative Analysis of Spatial Transcriptome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A rare PRIMER cell state in plant immunity.Nature · 2025Article
- Opportunities and challenges in the application of spatiotemporal transcriptomics in plant research.Frontiers in plant science · 2025Review
- Quantitative and spatially resolved detection of multiplexed microRNA from plant tissue via hybridization to hydrogel-bound DNA probes in nanoliter well arrays.Microsystems & nanoengineering · 2024Article
- Spatial metatranscriptomics resolves host-bacteria-fungi interactomes.Nature biotechnology · 2024Article
- Opportunities and Challenges in Advancing Plant Research with Single-cell Omics.Genomics, proteomics & bioinformatics · 2024Review
- Advances in Single-Cell Transcriptome Sequencing and Spatial Transcriptome Sequencing in Plants.Plants (Basel, Switzerland) · 2024Review
- Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis.Nature plants · 2024Article
- Plant biotechnology research with single-cell transcriptome: recent advancements and prospects.Plant cell reports · 2024Review
- The Shoot Apical Meristem: An Evolutionary Molding of Higher Plants.International journal of molecular sciences · 2024Review
- Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton.PloS one · 2024Article
- Spatially resolved transcriptomic analysis of the germinating barley grain.Nucleic acids research · 2023Article
- Understanding plant pathogen interactions using spatial and single-cell technologies.Communications biology · 2023Review
- Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap.Nature plants · 2023Article
- Single-cell and spatial multi-omics in the plant sciences: Technical advances, applications, and perspectives.Plant communications · 2023Review
- Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Elucidation of the complex processes involved in plant growth requires analysis of the spatial gene expression patterns in all affected tissues. This protocol extension is an adaptation of a protocol that describes how to use barcoded oligo-dT microarrays to evaluate spatial global gene expression profiles in mammalian tissue to enable it to be applied to plant material. Here, we explain the required adjustments for preparing and treating plant tissue sections on the array surface, specifically in regard to how to permeabilize and remove the tissue. Once the tissue has been removed, the cDNA-mRNA hybrid that is left on the slide is processed in the same way as cDNA obtained during experiments on mammalian tissue; thus the later stages of the protocol are not included here, and readers should follow the accompanying protocol for those. We have previously used our protocol to generate high-quality sequencing libraries for Arabidopsis thaliana inflorescence, Populus tremula developing and dormant leaf buds, and Picea abies female cones. However, we anticipate that the protocol can be adapted to other tissue types and species. The entire protocol for preparing samples and processing libraries can be completed in 3-4 d.
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Registered trials
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.