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In-situ Hybridization

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...

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Related Experiment Video

Updated: Jun 30, 2025

High Resolution Fluorescent In Situ Hybridization in Drosophila Embryos and Tissues Using Tyramide Signal Amplification

High Resolution Fluorescent In Situ Hybridization in Drosophila Embryos and Tissues Using Tyramide Signal Amplification

Published on: October 19, 2017

Mapping human tissues with highly multiplexed RNA in situ hybridization.

Kian Kalhor¹, Chien-Ju Chen^1,2, Ho Suk Lee^1,3

¹Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.

Nature Communications

|March 21, 2024

Summary

We developed DART-FISH, a new RNA mapping technology for large human tissues. This method profiles hundreds of genes in centimeter-sized sections, revealing cell types and disease states in the brain and kidney.

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Last Updated: Jun 30, 2025

High Resolution Fluorescent In Situ Hybridization in Drosophila Embryos and Tissues Using Tyramide Signal Amplification

High Resolution Fluorescent In Situ Hybridization in Drosophila Embryos and Tissues Using Tyramide Signal Amplification

Published on: October 19, 2017

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

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Published on: August 14, 2018

Whole Mount RNA Fluorescent in situ Hybridization of Drosophila Embryos

Whole Mount RNA Fluorescent in situ Hybridization of Drosophila Embryos

Published on: January 30, 2013

Area of Science:

Molecular Biology
Genomics
Neuroscience

Background:

In situ transcriptomic techniques offer insights into tissue organization and cell interactions.
Existing multiplexed RNA in situ mapping methods have limitations for large human tissues, including size, quality, and autofluorescence.

Purpose of the Study:

To develop a novel in situ transcriptomic technology for profiling large human tissue sections.
To overcome limitations of existing methods for analyzing human tissue at the RNA level.

Main Methods:

Developed DART-FISH (Digital Analysis of RNA by Fluorescence In Situ Hybridization), a padlock probe-based technology.
Introduced an omni-cell type cytoplasmic stain for improved cell body segmentation.
Utilized an enzyme-free isothermal decoding procedure for rapid gene imaging.

Main Results:

Successfully profiled hundreds to thousands of genes in centimeter-sized human tissue sections.
Mapped 121 genes in large human neocortex sections in under 10 hours, recapitulating 20 neuronal and non-neuronal subclasses.
Mapped 300 genes in diseased human kidney tissue, identifying over 20 healthy and pathological cell states and diseased niches.

Conclusions:

DART-FISH enables high-throughput gene profiling in large human tissues, overcoming previous technical barriers.
The technology accurately maps cellular architecture and identifies distinct cell states in both healthy and diseased human organs.
This advancement facilitates deeper understanding of human tissue biology and disease mechanisms.