Definition and research guide
This page combines a MeSH definition, publication statistics and selected research abstracts. It is a starting point for reading the literature, not a medical textbook or a systematic evidence review.
Content available: 4 complete abstracts (723 words), 10 references. Full article text is not stored or reproduced here; follow the PMID, DOI or PMC links to read the original sources and their access terms.
Definition
A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.
Definition: NLM Medical Subject Headings (MeSH) scope note (Public domain (U.S. National Library of Medicine); attribution requested). View the MeSH record.
Also known as: Hybridization, In Situ; Hybridizations, In Situ; In Situ Hybridizations; Hybridization in Situ.
Where it fits in the MeSH classification
- Broader topics
- Staining and Labeling; Spatial Transcriptomics; Nucleic Acid Hybridization
- Narrower topics
- In Situ Hybridization, Fluorescence; Primed In Situ Labeling
Research landscape
PubMed indexes 100,374 records tagged with the MeSH heading “In Situ Hybridization” (counts retrieved 2026-10-29). 7,250 of them (7.2%) were published from 2020 onward, and the busiest period so far is 2000-2009 with 41,362 records.
Reviews account for 4,204 records (4.2%) and meta-analyses for 62. Randomized controlled trials number 253 (0.3%) as a share of all records on the topic. Randomized trials make up only a small share of this literature, so much of what is known comes from laboratory, observational or descriptive work.
Show the data
| Period | Records |
|---|---|
| through 1999 | 28,049 |
| 2000-2009 | 41,362 |
| 2010-2019 | 23,713 |
| 2020 onward | 7,250 |
Publication-type chart data
| Type | Records | Share |
|---|---|---|
| Reviews | 4,204 | 4.2% |
| Meta-analyses | 62 | 0.1% |
| Randomized controlled trials | 253 | 0.3% |
Method: PubMed query "In Situ Hybridization"[MeSH Terms] with publication-type and date filters, retrieved 2026-10-29.
Reading the evidence in genetics and genomics
Genetic findings vary widely in strength. A variant linked to a condition in one study may not replicate in other ancestries, and most common variants have small effects that are meaningful only in aggregate. Studies of rare, high-impact variants can support strong causal claims about a gene, while association studies describe statistical links that need functional and independent replication. Check the sample size, the ancestry of participants, whether results were replicated, and whether a laboratory or clinical outcome was actually measured.
Evidence from open-access studies
These open-access studies come from PubMed’s best-match results for this heading (papers whose main topic it is), ranked here by citation count, with one recent addition. Each abstract is reproduced in full under its recorded open licence so that you can read the authors’ own words. They illustrate the literature; they are not a systematic summary of it. Citation counts measure attention, not reliability or clinical benefit.
| Study / authors | Year | Source label / design | Europe PMC citations | Licence / source |
|---|---|---|---|---|
| Giotto: a toolbox for integrative analysis and visualization of spatial expression data | 2021 | Research article Design not recorded in structured metadata | 873 | cc by PMID 33685491 · DOI · PMC7938609 |
| Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH | 2021 | Research article Design not recorded in structured metadata | 462 | cc by PMID 34616063 · DOI · PMC8494645 |
| Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers | 2020 | Research article Design not recorded in structured metadata | 213 | cc by PMID 33037211 · DOI · PMC7547110 |
| Social lives of bacteria as revealed through CLASI-FISH | 2026 | Review article Design not recorded in structured metadata | 1 | cc by PMID 42614111 · DOI · PMC13538133 |
Giotto: a toolbox for integrative analysis and visualization of spatial expression data [1]
Abstract reading summary — source excerpts
- Opening excerpt
- Spatial transcriptomic and proteomic technologies have provided new opportunities to investigate cells in their native microenvironment.
- Closing excerpt
- To demonstrate its general applicability, we apply Giotto to a wide range of datasets encompassing diverse technologies and platforms.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (98 words)
Spatial transcriptomic and proteomic technologies have provided new opportunities to investigate cells in their native microenvironment. Here we present Giotto, a comprehensive and open-source toolbox for spatial data analysis and visualization. The analysis module provides end-to-end analysis by implementing a wide range of algorithms for characterizing tissue composition, spatial expression patterns, and cellular interactions. Furthermore, single-cell RNAseq data can be integrated for spatial cell-type enrichment analysis. The visualization module allows users to interactively visualize analysis outputs and imaging features. To demonstrate its general applicability, we apply Giotto to a wide range of datasets encompassing diverse technologies and platforms.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 33685491 · DOI · PMC7938609
Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH [2]
Abstract reading summary — source excerpts
- Opening excerpt
- A mammalian brain is composed of numerous cell types organized in an intricate manner to form functional neural circuits.
- Closing excerpt
- Furthermore, we integrated MERFISH with retrograde labelling to probe projection targets of neurons of the mouse primary motor cortex and found that their cortical projections formed a complex network in which individual neuronal clusters project to multiple target regions and individual target regions receive inputs from multiple neuronal clusters.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (232 words)
A mammalian brain is composed of numerous cell types organized in an intricate manner to form functional neural circuits. Single-cell RNA sequencing allows systematic identification of cell types based on their gene expression profiles and has revealed many distinct cell populations in the brain1,2. Single-cell epigenomic profiling3,4 further provides information on gene-regulatory signatures of different cell types. Understanding how different cell types contribute to brain function, however, requires knowledge of their spatial organization and connectivity, which is not preserved in sequencing-based methods that involve cell dissociation. Here we used a single-cell transcriptome-imaging method, multiplexed error-robust fluorescence in situ hybridization (MERFISH)5, to generate a molecularly defined and spatially resolved cell atlas of the mouse primary motor cortex. We profiled approximately 300,000 cells in the mouse primary motor cortex and its adjacent areas, identified 95 neuronal and non-neuronal cell clusters, and revealed a complex spatial map in which not only excitatory but also most inhibitory neuronal clusters adopted laminar organizations. Intratelencephalic neurons formed a largely continuous gradient along the cortical depth axis, in which the gene expression of individual cells correlated with their cortical depths. Furthermore, we integrated MERFISH with retrograde labelling to probe projection targets of neurons of the mouse primary motor cortex and found that their cortical projections formed a complex network in which individual neuronal clusters project to multiple target regions and individual target regions receive inputs from multiple neuronal clusters.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 34616063 · DOI · PMC8494645
Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers [3]
Abstract reading summary — source excerpts
- Opening excerpt
- Skeletal muscle fibers are large syncytia but it is currently unknown whether gene expression is coordinately regulated in their numerous nuclei.
- Closing excerpt
- These findings highlight a previously undefined mechanism of coordination of gene expression in a syncytium.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (147 words)
Skeletal muscle fibers are large syncytia but it is currently unknown whether gene expression is coordinately regulated in their numerous nuclei. Here we show by snRNA-seq and snATAC-seq that slow, fast, myotendinous and neuromuscular junction myonuclei each have different transcriptional programs, associated with distinct chromatin states and combinations of transcription factors. In adult mice, identified myofiber types predominantly express either a slow or one of the three fast isoforms of Myosin heavy chain (MYH) proteins, while a small number of hybrid fibers can express more than one MYH. By snRNA-seq and FISH, we show that the majority of myonuclei within a myofiber are synchronized, coordinately expressing only one fast Myh isoform with a preferential panel of muscle-specific genes. Importantly, this coordination of expression occurs early during post-natal development and depends on innervation. These findings highlight a previously undefined mechanism of coordination of gene expression in a syncytium.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 33037211 · DOI · PMC7547110
Social lives of bacteria as revealed through CLASI-FISH [4]
Abstract reading summary — source excerpts
- Opening excerpt
- The spatial organization of microbiomes illuminates their structure, function, and relationship to their host.
- Closing excerpt
- Collectively, visualizing the spatial organization of host-associated microbiomes reveals spatial relationships among taxa and between microbes and host and serves to generate predictions about the dynamics of the host-microbiome interaction.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (246 words)
The spatial organization of microbiomes illuminates their structure, function, and relationship to their host. Using fluorescence spectral imaging to discriminate up to 16 fluorophores and using combinations of probes to generate unique spectral signatures, combinatorial labeling and spectral imaging-fluorescence in situ hybridization (CLASI-FISH) has been deployed to analyze spatial organization in oral, gut, and marine microbiomes. In dental plaque, imaging revealed the structural role of Corynebacterium matruchotii in organizing the plaque biofilm and revealed previously unrecognized complexity in dental plaque corncob structures. Tongue dorsum biofilms showed a patchy organization around a core of host epithelial cells projecting from the tongue surface, with anaerobes located near the core and oxygen-tolerant taxa near the surface. Taxa that are prominent in these tongue dorsum communities can reduce nitrate to nitrite and thus may play an important role in human nitrate metabolism. In contrast with the highly structured organization of oral biofilms, analysis of the gut microbiome by CLASI-FISH showed a mixed community, indicating that the rate of mixing in the gut is high enough to overcome the tendency of bacterial replication to generate single-taxon patches. Application of CLASI-FISH to blades of kelp showed a dense biofilm with clusters of cocci near the kelp surface, bacteria invading the kelp tissue, and rod-shaped and filamentous bacteria extending into the water column. Collectively, visualizing the spatial organization of host-associated microbiomes reveals spatial relationships among taxa and between microbes and host and serves to generate predictions about the dynamics of the host-microbiome interaction.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 42614111 · DOI · PMC13538133
Key reviews and meta-analyses
The most cited review-type papers among PubMed’s best-match results for this heading, listed with bibliographic details only. Follow the links for the full text and access terms.
- Research article Target-enrichment strategies for next-generation sequencing [5]
- Research article Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques [6]
- Research article LNA: a versatile tool for therapeutics and genomics [7]
- Research article Fluorescence in situ hybridization: past, present and future [8]
- Research article Comparison of telomere length measurement methods [9]
- Research article HER2 in situ hybridization in breast cancer: clinical implications of polysomy 17 and genetic heterogeneity [10]
References
- Dries R, Zhu Q, Dong R, Eng CL, Li H, Liu K, et al.. Giotto: a toolbox for integrative analysis and visualization of spatial expression data. . 2021. PMID 33685491 · DOI · PMC7938609
- Zhang M, Eichhorn SW, Zingg B, Yao Z, Cotter K, Zeng H, et al.. Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH. . 2021. PMID 34616063 · DOI · PMC8494645
- Dos Santos M, Backer S, Saintpierre B, Izac B, Andrieu M, Letourneur F, et al.. Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers. . 2020. PMID 33037211 · DOI · PMC7547110
- Mark Welch JL. Social lives of bacteria as revealed through CLASI-FISH. . 2026. PMID 42614111 · DOI · PMC13538133
- Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, et al.. Target-enrichment strategies for next-generation sequencing. Nat Methods. 2010. PMID 20111037 · DOI
- Amann R, Fuchs BM. Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol. 2008. PMID 18414500 · DOI
- Petersen M, Wengel J. LNA: a versatile tool for therapeutics and genomics. Trends Biotechnol. 2003. PMID 12573856 · DOI
- Levsky JM, Singer RH. Fluorescence in situ hybridization: past, present and future. J Cell Sci. 2003. PMID 12808017 · DOI
- Lai TP, Wright WE, Shay JW. Comparison of telomere length measurement methods. Philos Trans R Soc Lond B Biol Sci. 2018. PMID 29335378 · DOI · PMC5784071
- Hanna WM, Rüschoff J, Bilous M, Coudry RA, Dowsett M, Osamura RY, et al.. HER2 in situ hybridization in breast cancer: clinical implications of polysomy 17 and genetic heterogeneity. Mod Pathol. 2014. PMID 23807776 · DOI
About this article
- Sources
- NLM Medical Subject Headings (definition, synonyms); NCBI PubMed (counts, identifiers); Europe PMC (open-access abstracts and citation counts).
- Verification
- Every reference was resolved against PubMed on 2026-10-31; title, year and DOI matched.
- Review state
- automated source verified; no human expert review has been recorded yet.
- Version
- 1, last updated 2026-10-29.
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Evidence strength
EvidenceHelix's computed view of the study designs behind this topic: how common meta-analyses, randomized trials and reviews are, how recent the literature is, and a plain-language reading. It describes the design mix of the literature. It is not a quality appraisal of any study, and it is not medical advice.