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Related Concept Videos

In-situ Hybridization02:31

In-situ Hybridization

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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...
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FISH - Fluorescent In-situ Hybridization02:07

FISH - Fluorescent In-situ Hybridization

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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: Jan 14, 2026

MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as A Novel Detection and Quantification Method
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MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as A Novel Detection and Quantification Method

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RNA In situ Hybridization with Sequential Protein Immunofluorescence in Tandem Assay.

Danielle L Stolley1, Anna K Casasent1, Basant T Gamal2

  • 1Department of Hematopoietic Biology & Malignancy, The University of Texas MD Anderson Cancer Center.

Journal of Visualized Experiments : Jove
|October 27, 2025
PubMed
Summary

This study introduces seqRNA-ISH+seqIF, a novel spatial multi-omics method. It simultaneously analyzes RNA and protein expression, revealing cellular coordination and disease mechanisms.

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Area of Science:

  • Cellular Biology
  • Molecular Biology
  • Biotechnology

Background:

  • Cellular function relies on coordinated molecular signals, not isolated ones.
  • Understanding cell-cell interactions and disease progression requires integrated spatial multi-omics.
  • Analyzing both RNA and protein in situ provides insights into cellular instructions and execution within a microenvironment.

Purpose of the Study:

  • To develop and present a novel spatial multi-omics platform for high-throughput protein and RNA investigation.
  • To enable simultaneous analysis of RNA and protein expression within their native tissue context.
  • To facilitate a deeper understanding of cellular communication and disease mechanisms through integrated spatial analysis.

Main Methods:

  • Integration of sequential immunofluorescence (SeqIF) with RNA in situ hybridization (ISH).
  • Utilized an on-tissue microfluidics-driven system for targeted multi-omics analysis.
  • Developed a platform (seqRNA-ISH+seqIF) capable of analyzing up to 12 RNA and 24 protein targets in a single run.

Main Results:

  • The seqRNA-ISH+seqIF method allows for high-throughput, sequential, targeted protein and RNA analysis in a spatial context.
  • The platform bypasses the need for fluorophore compatibility considerations and extensive optimization for high-plexing.
  • Enables precise examination of RNA-protein interactions and validation of whole transcriptome methods.

Conclusions:

  • The developed platform offers a powerful tool for dissecting cellular coordination and microenvironmental interactions.
  • This targeted spatial multi-omics approach enhances our understanding of how cells execute instructions within their niche.
  • seqRNA-ISH+seqIF provides a precise method for studying disease progression by integrating molecular and spatial information.