ArticleCurrent protocols2025
Imaging the Intestinal Transcriptome With Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH).
Article in Current protocols, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
7 citing papers in PubMed.
- RNA-aware tissue preservation workflows for high-quality spatial transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- An image-based transcriptomics atlas reveals the regional and microbiota-dependent molecular, cellular, and spatial structure of the murine gut.Cell host & microbe · 2026Article
- Beyond Structure: The Dynamic Role of the Extracellular Matrix Components in Immune Evasion.Cancer communications (London, England) · 2026Review
- Brain-immune interactions generate pathogen-specific sickness states.bioRxiv : the preprint server for biology · 2025Article
- The Human Archaeome: Commensals, Opportunists, or Emerging Pathogens?Pathogens (Basel, Switzerland) · 2025Review
- Protocol optimization improves the performance of multiplexed RNA imaging.Scientific reports · 2025Article
- In situ profiling of plasma cell clonality with image-based single-cell transcriptomics.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Multiplexed error-robust fluorescence in situ hybridization (MERFISH) is a massively multiplexed single RNA-molecule imaging technique capable of spatially resolved single-cell transcriptomic profiling of thousands of genes in millions of cells within intact tissue slices. Initially introduced for brain tissues, MERFISH has since been extended to other tissues, where rapid RNA degradation during the preparation process can pose challenges. This protocol outlines the application of MERFISH in one such challenging tissue, the mammalian gastrointestinal tract. We describe two complementary protocols leveraging either fresh frozen or fixed frozen approaches and describe methods for combining RNA imaging with immunofluorescence. While these protocols were designed and validated in gut tissues, we anticipate that they will be useful resources for the application to other challenging tissue types. © 2025 Wiley Periodicals LLC. Basic Protocol 1: Fixed-frozen sample preparation Basic Protocol 2: Fresh-frozen sample preparation Basic Protocol 3: Encoding probe construction Basic Protocol 4: MERFISH imaging Basic Protocol 5: Image decoding Support Protocol 1: Coverslip silanization Support Protocol 2: Poly-d-lysine (PDL) coating of the coverslips Support Protocol 3: Hybridization buffer preparation Support Protocol 4: Trolox quinone stock preparation Support Protocol 5: TCEP stock preparation Alternate Protocol 1: MERFISH-compatible immunofluorescent boundary stains in fresh frozen tissue Alternate Protocol 2: Immunofluorescent boundary stains with methacrylate-NHS-anchored antibodies for PFA-fixed samples Alternate Protocol 3: Guanidine-HCl tissue clearing.
Indexed as
Identifiers
What OpenQuestion holds
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.