In Situ Detection
In Situ Detection - Related Videos
04:46
In Situ Detection of Bacteria in Mouse Gingival Tissue Sections
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2026
Source: Choi, Y. S., et al. In Situ Detection of Bacteria within Paraffin-embedded Tissues Using a Digoxin-labeled DNA Probe Targeting 16S rRNA. J. Vis. Exp. (2015).This video demonstrates the in situ detection of bacteria in mouse gingival tissue sections using digoxin-labeled DNA probes targeting bacterial DNA. The section is incubated with the probe. Alkaline phosphatase-conjugated antibodies specific to digoxin are added. Endogenous phosphatases are inactivated, and a colored precipitate is...
09:10
Combination of Adhesive-tape-based Sampling and Fluorescence in situ Hybridization for Rapid Detection of Salmonella on Fresh Produce
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Cited by 17 •
2010
This protocol describes a simple adhesive-tape-based approach for sampling of tomato and other fresh produce surfaces, followed by rapid whole cell detection of Salmonella using fluorescence in situ hybridization (FISH).
08:00
Whole-Mount In Situ Hybridization
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2023
Whole-mount in situ hybridization (WMISH) is a common technique used for visualizing the location of expressed RNAs in embryos. In this process, synthetically produced RNA probes are first complementarily bound, or "hybridized," to the transcripts of target genes. Immunohistochemistry or fluorescence is then used to detect these RNA hybrids, revealing spatial and temporal patterns of gene expression. Unlike traditional in situ hybridization techniques, which require thin tissue sections whose...
06:00
HCR-DNA FISH: A Fluorescence In Situ Hybridization Technique to Detect Viral DNA in Infected Cells
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2023
In this video, the cells infected with MCPyV virions were subjected to in situ hybridization chain reaction to detect MCPyV specific genomes. Further, the DNA-HCR technique was combined with FISH to visualize the MCPyV DNA in infected human skin cells.
10:26
RNAscope for In situ Detection of Transcriptionally Active Human Papillomavirus in Head and Neck Squamous Cell Carcinoma
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Cited by 41 •
2014
The presence of high-risk HPV in head and neck tumor tissue is associated with favorable outcomes. The recently developed RNA in situ hybridization technique called RNAscope allows direct visualization of HPV E6/E7 mRNA in FFPE tissue sections.
FAQs
Selectivity comes from matching a labeled probe, antibody, or reporter to the molecule, cell type, or biological activity being examined. Binding identifies the intended target while the surrounding tissue or cellular structure remains visible. This combination allows researchers to distinguish target-positive regions from neighboring areas and relate molecular presence to the organization of the specimen.
Signal generation determines how the detected target becomes visible at its location. Fluorescence, colorimetric, and enzymatic approaches can reveal binding directly within the specimen, but they present the result through different visual outputs. Selecting an appropriate signal supports clearer interpretation of where the target occurs and how its distribution relates to tissue architecture.
Bulk measurements can indicate whether a target is present in a combined sample, but they may not show which cells or tissue regions contain it. In situ detection retains spatial relationships, making it possible to compare neighboring cells, anatomical regions, and local signaling events. That added context can explain patterns that an overall abundance measurement alone cannot resolve.
A general workflow begins with a specimen in its native tissue, cellular, or organismal context, followed by application of a target-selective probe, antibody, or reporter. The bound detection element is then visualized through fluorescence, colorimetric, or enzymatic signal generation. Researchers interpret the resulting signal by considering its location alongside the specimen’s preserved structure.
This approach is useful when the research question depends on location as well as presence. It can support studies of development, disease characterization, biomarker analysis, and validation of molecular assays. By showing where genes, proteins, pathogens, or signaling events occur, the method connects molecular findings with tissue organization and the identities or positions of nearby cells.
Results can reveal whether a target is concentrated in particular regions, associated with specific cells, or positioned near other biologically relevant structures. Such patterns help researchers examine tissue organization and local biological activity rather than relying only on specimen-wide measurements. The observations can also provide spatial evidence for interpreting or validating findings from molecular assays.