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Related Concept Videos

In-situ Hybridization02:31

In-situ Hybridization

In situ hybridization (ISH) is a technique used to detect and localize specific DNA or RNA molecules in cells, tissue, or tissue sections using a labeled probe. The technique was first used in 1969 for the investigation of nucleic acids. It is currently an essential tool in scientific research and clinical settings, especially for diagnostic purposes.
Types of probes and labels
A probe is a complementary strand of DNA or RNA that binds to corresponding nucleotide sequences in a cell. Many...
FISH - Fluorescent In-situ Hybridization02:07

FISH - Fluorescent In-situ Hybridization

Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...

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Related Experiment Video

Updated: Jun 27, 2026

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay
10:57

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay

Published on: August 14, 2018

From Molecular Visualization to Spatial Landscapes: Engineering the Next Generation of In Situ Hybridization.

Zejia Li1, Miaomiao Luo2, Minshuai Zhu2

  • 1College of Art, Zhejiang Normal University, Jinhua 321004, China.

Genes
|June 26, 2026
PubMed
Summary

In situ hybridization (ISH) has evolved into advanced spatial transcriptomics, enabling sensitive RNA detection in intact tissues. Modern ISH methods offer powerful insights beyond traditional approaches for various biological studies.

Keywords:
HCR-FISHMERFISHRAEFISHRNAscopecell segmentationin situ hybridizationsingle-molecule imagingspatial multi-omicsspatial transcriptomics

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In Situ Hybridization for the Precise Localization of Transcripts in Plants
12:15

In Situ Hybridization for the Precise Localization of Transcripts in Plants

Published on: November 23, 2011

Related Experiment Videos

Last Updated: Jun 27, 2026

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay
10:57

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay

Published on: August 14, 2018

In Situ Hybridization for the Precise Localization of Transcripts in Plants
12:15

In Situ Hybridization for the Precise Localization of Transcripts in Plants

Published on: November 23, 2011

Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • In situ hybridization (ISH) has transformed from a basic staining method to a sophisticated technique for molecular detection in cells and tissues.
  • Advances in probe design, signal amplification, and imaging have propelled ISH into a key technology for spatial transcriptomics.
  • Modern ISH methods allow for sensitive, specific, and multiplexed RNA detection within preserved cellular and tissue architecture.

Purpose of the Study:

  • To review the molecular and engineering principles behind modern ISH methods and their application in spatial profiling.
  • To analyze the strengths and limitations of various ISH-based techniques, including sensitivity, specificity, and cost.
  • To discuss the impact of ISH advancements on spatial transcriptomics and biological insights.

Main Methods:

  • Review of hybridization chain reaction, branched-DNA amplification, SABER-FISH, rolling-circle-amplification, seqFISH, MERFISH, and RAEFISH.
  • Examination of probe design, signal amplification, cyclic imaging, combinatorial barcoding, and computational decoding.
  • Consideration of sequencing-based spatial capture platforms for comparative benchmarking.

Main Results:

  • Modern ISH methods provide sensitive, specific, and multiplexed RNA detection in intact cells and tissues.
  • ISH-based spatial profiling enables spatially resolved transcriptomic analysis, offering insights not achievable with bulk or single-cell methods.
  • Benchmarking and standardization efforts are defining quantitative criteria for comparing ISH platforms.

Conclusions:

  • In situ hybridization has evolved into a versatile framework for in situ detection and spatially resolved transcriptomic analysis.
  • Modern ISH methods and spatial profiling are crucial for applications in neuroscience, cancer, developmental biology, and functional genomics.
  • These advanced techniques provide unique information by preserving cellular and tissue architecture during molecular analysis.