ArticleScientific reports2018
Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 155 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
155 citing papers in PubMed, 261 citations in OpenAlex.
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- APEX-seq maps transcriptome-wide subcellular RNA localization in living cells.Nature protocols · 2026Review
- Imaging-Based Spatial Transcriptomics: Data Interpretation Methods and Biomedical Applications.Biology · 2026Review
- Multi-Dimensional Transcriptomics Reveals the Prominent Role of Neuroinflammation in Alzheimer's Disease.International journal of molecular sciences · 2026Review
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- RESCUE: recovery of unattributed expression patterns in spatial transcriptomics.Nature communications · 2026Article
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- Seq-Scope-eXpanded: spatial omics beyond optical resolution.Nature communications · 2026Article
- Expansion omics: from expansion microscopy to spatial omics.Molecular systems biology · 2026Review
- Principles ofbioRxiv : the preprint server for biology · 2026Article
- 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
- PRIMER cells: a new weapon in plant immunity research.Die Naturwissenschaften · 2026Review
- Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications.Cancer cell · 2026Review
- Reimagining the Synthetic Biology DBTL Cycle with Machine Learning.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Applications and development of in situ nucleic acid visualization techniques.Frontiers in bioengineering and biotechnology · 2026Review
- From cellular heterogeneity to precision medicine: single-cell multi-omics in CNS disease research.Frontiers in cellular neuroscience · 2026Review
- Article
95 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
As an image-based single-cell transcriptomics approach, multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows hundreds to thousands of RNA species to be identified, counted and localized in individual cells while preserving the native spatial context of RNAs. In MERFISH, RNAs are identified via a combinatorial labeling approach that encodes RNA species with error-robust barcodes followed by sequential rounds of single-molecule FISH (smFISH) to read out these barcodes. The accuracy of RNA identification relies on spatially separated signals from individual RNA molecules, which limits the density of RNAs that can be measured and makes the multiplexed imaging of a large number of high-abundance RNAs challenging. Here we report an approach that combines MERFISH and expansion microscopy to substantially increase the total density of RNAs that can be measured. Using this approach, we demonstrate accurate identification and counting of RNAs, with a near 100% detection efficiency, in a ~130-RNA library composed of many high-abundance RNAs, the total density of which is more than 10 fold higher than previously reported. In parallel, we demonstrate the combination of MERFISH with immunofluorescence in expanded samples. These advances increase the versatility of MERFISH and will facilitate its application to a wide range of biological problems.
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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.