ArticleMethods in enzymology2016
RNA Imaging with Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH).
Article in Methods in enzymology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 138 papers, 2 of them syntheses that pooled it.
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Who cites it
138 citing papers in PubMed, 2 syntheses or guidelines pooled it, 226 citations in OpenAlex.
- Enhancing RNA Capture Efficiency in Spatial Transcriptomics: A Review of Innovative Technologies and Strategies.International journal of molecular sciences · 2025Pooled it
- Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain.Scientific reports · 2023Pooled it
- Advancing the Deciphering of Host-Microbe Crosstalk with Spatial Omics: A Mini-Review.Current microbiology · 2026Review
- Single-cell multiome profiling reveals neuronal bias of modulatory role of MeCP2 phosphorylation.Neurobiology of disease · 2026Article
- Spatial Immune Coding in Tumor-Draining Lymph Nodes: Functional Compartmentalization of Immune Activation and Immunosuppression.International journal of molecular sciences · 2026Review
- Fast, StreamlinedChemical & biomedical imaging · 2026Article
- Spatial Transcriptomics for Dissecting Cellular and Molecular Heterogeneity in the Aging and Diseased Brain.International journal of molecular sciences · 2026Review
- STRESS: spatial transcriptomics resolution enhancing method based on the state-space model.Briefings in bioinformatics · 2026Article
- Review
- FINDER converts zero-background kinetic fingerprinting into area-scalable attomolar biomarker detection.Research square · 2026Article
- Spatial architecture of autism pathogenesis reveals mosaic structural disarray during early development.Nature communications · 2026Article
- FINDER converts zero-background kinetic fingerprinting into area-scalable attomolar biomarker detection.bioRxiv : the preprint server for biology · 2026Article
- Review
- Spatial mapping of microbial communities by an integrated automation platform of sequential FISH.Cell reports methods · 2026Article
- autoFISH: a modular toolbox for sequential single-molecule RNA FISH experiments.Communications biology · 2026Article
- Modern RNA Quantification Methods: From RT-qPCR to Advanced Microscopy.The journal of physical chemistry. B · 2026Review
- The Kinetic Intron Hypothesis.bioRxiv : the preprint server for biology · 2026Article
- S2potAE: multimodal spatial spot autoencoder integrating image and transcriptomic features for deconvolution.Briefings in bioinformatics · 2026Article
- Haruka Resolves Perturbation Response Heterogeneity in Spatial Cell Niches.bioRxiv : the preprint server for biology · 2025Article
- Cell-type deconvolution methods for spatial transcriptomics.Nature reviews. Genetics · 2025Review
78 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Quantitative measurements of both the copy number and spatial distribution of large fractions of the transcriptome in single cells could revolutionize our understanding of a variety of cellular and tissue behaviors in both healthy and diseased states. Single-molecule fluorescence in situ hybridization (smFISH)-an approach where individual RNAs are labeled with fluorescent probes and imaged in their native cellular and tissue context-provides both the copy number and spatial context of RNAs but has been limited in the number of RNA species that can be measured simultaneously. Here, we describe multiplexed error-robust fluorescence in situ hybridization (MERFISH), a massively parallelized form of smFISH that can image and identify hundreds to thousands of different RNA species simultaneously with high accuracy in individual cells in their native spatial context. We provide detailed protocols on all aspects of MERFISH, including probe design, data collection, and data analysis to allow interested laboratories to perform MERFISH measurements themselves.
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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.