ArticleScientific reports2019
Multiplexed detection of RNA using MERFISH and branched DNA amplification.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers, 1 of them a synthesis that pooled it.
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Who cites it
112 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Enhancing RNA Capture Efficiency in Spatial Transcriptomics: A Review of Innovative Technologies and Strategies.International journal of molecular sciences · 2025Pooled it
- Integrative single-cell and spatial transcriptomic approaches to decipher the tumor microenvironment and therapeutic resistance in pancreatic cancer.Cancer biology & therapy · 2026Review
- Article
- Unveiling the role of spatial transcriptomics in the analysis of the tumor immune microenvironment (Review).International journal of molecular medicine · 2026Review
- Computational analysis in spatial transcriptomics: methods and perspectives.Briefings in bioinformatics · 2026Review
- Single-cell RNA sequencing in stroke and traumatic brain injury: Current achievements, challenges and future perspectives on transcriptomic profiling.Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism · 2026Review
- CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments.PLoS computational biology · 2026Article
- Article
- N-Orbit: towards a universal model and metric for comparing tissue microenvironments.Nature communications · 2026Article
- GatorDuo: Global-Consistency Dual-Graph Refinement With Pseudo-Label Agreement for Spatial Transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- autoFISH: a modular toolbox for sequential single-molecule RNA FISH experiments.Communications biology · 2026Article
- Spatial Multiomics Combining Lipids and Gene Expression Using MALDI ISH MSI.Analytical chemistry · 2026Article
- Dissecting Normal and Abnormal Human Kidney Development Using Multiomics.Journal of the American Society of Nephrology : JASN · 2026Review
- Developing a Robust Multiround HCR-FISH Method Modified for Caenorhabditis elegans.Genes to cells : devoted to molecular & cellular mechanisms · 2026Article
- Mapping multipathology via spatial omic integration.Current opinion in biotechnology · 2026Review
- Super-resolved, three-dimensional spatial transcriptomics reveals cell-type and brain-region-specific modulation of key epitranscriptomic switches following adolescent alcohol exposure.bioRxiv : the preprint server for biology · 2026Article
- AI-Based Prediction of Gene Expression in Single-Cell and Multiscale Genomics and Transcriptomics.International journal of molecular sciences · 2026Review
- Fibroblasts in the tumor microenvironment: heterogeneity and dynamic interactions in tumor progression revealed by spatial transcriptomics.Cellular oncology (Dordrecht, Netherlands) · 2025Review
- GPU-accelerated, self-optimizing processing for 3D multiplexed iterative RNA-FISH experiments.bioRxiv : the preprint server for biology · 2025Article
52 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
Multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows simultaneous imaging of numerous RNA species in their native cellular environment and hence spatially resolved single-cell transcriptomic measurements. However, the relatively modest brightness of signals from single RNA molecules can become limiting in a number of applications, such as increasing the imaging throughput, imaging shorter RNAs, and imaging samples with high degrees of background, such as some tissue samples. Here, we report a branched DNA (bDNA) amplification approach for MERFISH measurements. This approach produces a drastic signal increase in RNA FISH samples without increasing the fluorescent spot size for individual RNAs or increasing the variation in brightness from spot to spot, properties that are important for MERFISH imaging. Using this amplification approach in combination with MERFISH, we demonstrated RNA imaging and profiling with a near 100% detection efficiency. We further demonstrated that signal amplification improves MERFISH performance when fewer FISH probes are used for each RNA species, which should allow shorter RNAs to be imaged. We anticipate that the combination of bDNA amplification with MERFISH should facilitate many other applications and extend the range of biological questions that can be addressed by this technique in both cell culture and tissues.
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