ArticleNature biotechnology2023
Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers, 1 of them a synthesis that pooled it.
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Who cites it
71 citing papers in PubMed, 1 synthesis or guideline pooled it, 106 citations in OpenAlex.
- Cross-expression meta-analysis of mouse brain slices reveals coordinated gene expression across spatially adjacent cells.Genome biology · 2025Pooled it
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
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- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- NicheTrans: spatial-aware cross-omics translation.Nature methods · 2026Article
- Dissecting human organ development using spatial technologies.Developmental cell · 2026Review
- Advances in spatial omics for the analysis of prostate cancer.Analytical and bioanalytical chemistry · 2026Review
- Review
- SOFisher: reinforcement learning-guided experiment designs for spatial omics.Nature communications · 2026Article
- A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Spatially resolved in situ profiling of mRNA life cycle at transcriptome scale in intact cells and tissues using STARmap PLUS, RIBOmap and TEMPOmap.Nature protocols · 2026Review
- Cell neighborhood topology directs rare cell population identification.Nature communications · 2026Article
- Current landscape of single-cell genomics in meningioma.Neuro-oncology advances · 2026Review
- Macrophage retrotransposon expression is associated with lupus.Genes and immunity · 2026Article
- Applications and development of in situ nucleic acid visualization techniques.Frontiers in bioengineering and biotechnology · 2026Review
- Spatially Resolved Profiling of Compartmentalized Muscle and Brain Inflammation.European journal of immunology · 2025Review
- Review
- GPU-accelerated, self-optimizing processing for 3D multiplexed iterative RNA-FISH experiments.bioRxiv : the preprint server for biology · 2025Article
- Spatial Transcriptomics of Adipose Tissue: Technologies, Applications, and Challenges.Journal of obesity & metabolic syndrome · 2025Review
- Fluid-Squid: DIY Multiplexed Imaging of Cells and Tissues.bioRxiv : the preprint server for biology · 2025Article
11 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors at 3 institutions in 2 countries.
Funding
Abstract
Methods to spatially profile the transcriptome are dominated by a trade-off between resolution and throughput. Here we develop a method named Enhanced ELectric Fluorescence in situ Hybridization (EEL FISH) that can rapidly process large tissue samples without compromising spatial resolution. By electrophoretically transferring RNA from a tissue section onto a capture surface, EEL speeds up data acquisition by reducing the amount of imaging needed, while ensuring that RNA molecules move straight down toward the surface, preserving single-cell resolution. We apply EEL on eight entire sagittal sections of the mouse brain and measure the expression patterns of up to 440 genes to reveal complex tissue organization. Moreover, EEL can be used to study challenging human samples by removing autofluorescent lipofuscin, enabling the spatial transcriptome of the human visual cortex to be visualized. We provide full hardware specifications, all protocols and complete software for instrument control, image processing, data analysis and visualization.
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