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FISH - Fluorescent In-situ Hybridization

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,...

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: Jan 10, 2026

Visualizing Cell-to-cell Transfer of HIV using Fluorescent Clones of HIV and Live Confocal Microscopy

Visualizing Cell-to-cell Transfer of HIV using Fluorescent Clones of HIV and Live Confocal Microscopy

Published on: October 7, 2010

VISTA-FISH: Video Imaging with Spatial-Temporal Analysis by Fluorescent In Situ Hybridization.

Kun H Lee¹, Mingjia Yao¹, Javid Ghaemmaghami¹

¹Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

Biorxiv : the Preprint Server for Biology

|November 24, 2025

Summary

This summary is machine-generated.

We developed Video Imaging with Spatial-Temporal Analysis by FISH (VISTA-FISH) to link live cell imaging with gene expression. This method reveals molecular mechanisms of complex cellular functions and neuron activity.

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Area of Science:

Cell Biology
Neuroscience
Molecular Biology

Background:

Live-cell microscopy and gene expression analysis are vital for understanding dynamic cellular processes.
Traditional methods struggle to integrate temporal imaging with high-dimensional molecular data from the same cell.

Purpose of the Study:

To develop a novel technique integrating live-cell imaging with single-cell gene expression profiling.
To investigate the molecular underpinnings of cellular activity, organelle transport, and neuron function.

Main Methods:

Developed Video Imaging with Spatial-Temporal Analysis by FISH (VISTA-FISH) to correlate live-cell videos with end-point gene expression.
Applied VISTA-FISH to differentiating neurons to link activity, differentiation stage, and transcript localization.
Integrated pooled CRISPR interference screening with live-cell lysosome imaging.

Main Results:

Successfully linked neuron activity with differentiation stage, subcellular transcript localization, and cell subtype.
Built a predictive model for neuron activity based on gene expression data.
Identified gene expression and lysosome alterations in perturbed neurons using CRISPR screening.

Conclusions:

VISTA-FISH is a powerful tool for dissecting molecular mechanisms of complex temporal phenotypes.
The technique enables simultaneous analysis of live-cell dynamics and high-dimensional gene expression.
VISTA-FISH advances the study of neuron activity, organelle trafficking, and cellular functions.