ArticleFrontiers in neuroscience2023
Protecting RNA quality for spatial transcriptomics while improving immunofluorescent staining quality.
Article in Frontiers in neuroscience, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed, 9 citations in OpenAlex.
- Transforming subcellular spatial transcriptomics: deep learning models for cell segmentation.Nucleic acids research · 2026Review
- A New Tool to Decrease Interobserver Variability in Biomarker Annotation in Solid Tumor Tissue for Spatial Transcriptomic Analysis.Current issues in molecular biology · 2025Article
- Laser-capture microdissection for spatial transcriptomics of immunohistochemically detected neurons.The Journal of biological chemistry · 2025Article
- Spatial proteomics and transcriptomics characterization of tissue and multiple cancer types including decalcified marrow.Cancer biomarkers : section A of Disease markers · 2025Article
- RNA Stability: A Review of the Role of Structural Features and Environmental Conditions.Molecules (Basel, Switzerland) · 2024Review
- What can we learn about acid-base transporters in cancer from studying somatic mutations in their genes?Pflugers Archiv : European journal of physiology · 2024Review
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In comparison to bulk sequencing or single cell sequencing, spatial transcriptomics preserves the spatial information in tissue slices and can even be mapped to immunofluorescent stainings, allowing translation of gene expression information into their spatial context. This enables to unravel complex interactions of neighboring cells or to link cell morphology to transcriptome data. The 10× Genomics Visium platform offers to combine spatial transcriptomics with immunofluorescent staining of cryo-sectioned tissue slices. We applied this technique to fresh frozen mouse brain slices and developed a protocol that still protects RNA quality while improving buffers for immunofluorescent staining. We investigated the impact of various parameters, including fixation time and buffer composition, on RNA quality and antibody binding. Here, we propose an improved version of the manufacturer protocol, which does not alter RNA quality and facilitates the use of multiple additional antibodies that were not compatible with the manufacturer protocol before. Finally, we discuss the influence of various staining parameters, which contribute to the development of application specific staining protocols.
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