Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Map of spiking activity underlying change detection in the mouse visual system.

Cell·2026
Same author

Connecting single-cell transcriptomes to projectomes in the mouse visual cortex.

Nature·2026
Same author

Whole-neuron morphology and genetic identity define cell types and reveal principles of brain-wide connectivity.

Cell reports·2026
Same author

A layered standards framework for integrating single-cell and spatial omics data into brain cell atlases.

bioRxiv : the preprint server for biology·2026
Same author

Developmental dynamics of skeletal muscle can be recapitulated in vitro from pig embryonic stem cells.

Stem cell reports·2026
Same author

scVIP: personalized modeling of single-cell transcriptomes for developmental and disease phenotypes.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Jul 7, 2026

Genotyping and Quantification of In Situ Hybridization Staining in Zebrafish
05:41

Genotyping and Quantification of In Situ Hybridization Staining in Zebrafish

Published on: January 28, 2020

Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data.

Chang-Kyu Lee1, Susan M Sunkin, Chihchau Kuan

  • 1Allen Institute for Brain Science, Seattle, WA 98103, USA.

Genome Biology
|February 1, 2008
PubMed
Summary

This study presents a new method for quantifying colorimetric in situ hybridization (ISH) signals. This allows for large-scale comparisons between ISH gene expression data and microarray data.

More Related Videos

Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization
16:37

Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization

Published on: August 5, 2008

Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform
13:14

Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform

Published on: August 10, 2009

Related Experiment Videos

Last Updated: Jul 7, 2026

Genotyping and Quantification of In Situ Hybridization Staining in Zebrafish
05:41

Genotyping and Quantification of In Situ Hybridization Staining in Zebrafish

Published on: January 28, 2020

Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization
16:37

Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization

Published on: August 5, 2008

Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform
13:14

Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform

Published on: August 10, 2009

Area of Science:

  • Neuroscience
  • Bioinformatics
  • Genomics

Background:

  • Genome-wide gene expression data, such as from the Allen Brain Atlas, is increasingly available.
  • Colorimetric in situ hybridization (ISH) is a common method for visualizing gene expression.
  • Comparing ISH with quantitative methods like microarrays is crucial for data integration.

Purpose of the Study:

  • To develop a standardized method for relative quantification of colorimetric ISH signals.
  • To enable large-scale, cross-platform comparisons of gene expression data.
  • To assess the relationship between ISH and microarray-based gene expression modalities.

Main Methods:

  • Developed a novel computational method for standardized relative quantification of colorimetric ISH signal.
  • Applied the method to analyze genome-wide ISH data.
  • Compared the quantified ISH data with two publicly available microarray brain datasets.

Main Results:

  • Successfully established a standardized relative quantification method for colorimetric ISH.
  • Enabled large-scale cross-platform comparison of gene expression data.
  • Demonstrated the feasibility of integrating ISH and microarray data for expression level analysis.

Conclusions:

  • The novel quantification method facilitates robust comparison between ISH and microarray gene expression data.
  • This approach supports a more comprehensive understanding of gene expression across different technologies.
  • The findings contribute to the integration of diverse genomic datasets for brain research.