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

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
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...

You might also read

Related Articles

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

Sort by
Same author

Molecular evolution in light of regulatory-coding epistasis.

EMBO reports·2026
Same author

Predicting antifolate resistance in the unculturable fungal pathogen Pneumocystis jirovecii.

PLoS genetics·2026
Same author

A protein-fragment complementation assay to quantify synthetic protein scaffold efficiency.

Synthetic biology (Oxford, England)·2026
Same author

Mutational landscape and molecular bases of echinocandin resistance in Saccharomyces cerevisiae.

Genetics·2026
Same author

Paralog interference contributes to the preservation of genetic redundancy.

Current biology : CB·2026
Same author

Evolutionary causes and consequences of gene duplication.

Nature reviews. Genetics·2026

Related Experiment Video

Updated: Jun 14, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing.

Pierre Fontanillas1, Christian R Landry, Patricia J Wittkopp

  • 1Department of Ecology and Evolution, University of Lausanne, Switzerland. pierre.fontanillas@unil.ch

Molecular Ecology
|March 25, 2010
PubMed
Summary

Dissecting gene expression variation is key to understanding adaptation. This study determines the minimum sequencing depth needed for accurate allelic expression analysis in heterozygous individuals.

More Related Videos

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Related Experiment Videos

Last Updated: Jun 14, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Area of Science:

  • Evolutionary genetics
  • Genomics
  • Molecular biology

Background:

  • Phenotypic diversity arises from gene expression differences.
  • Allelic expression analysis provides deeper regulatory insights than total gene expression.
  • High-throughput sequencing enables genomic-scale allelic transcription studies.

Purpose of the Study:

  • To determine the minimum sequencing depth for accurate relative allelic expression measurement.
  • To establish the sequencing requirements for detecting allelic imbalance using high-throughput sequencing.
  • To apply allelic expression analysis to study cis-regulatory divergence in Drosophila.

Main Methods:

  • Mathematical modeling and computer simulations were used to assess statistical power.
  • Analysis focused on the influence of sequencing depth and allele assignment accuracy.
  • 454 sequencing was employed for a practical application in Drosophila.

Main Results:

  • A minimum of 500-1000 sequencing reads per gene are necessary to test for allelic imbalance within a species.
  • At least 5-10 million reads are required for genome-wide allelic expression studies of 10,000 genes.
  • The study demonstrated the feasibility of detecting cis-regulatory divergence using allelic expression.

Conclusions:

  • Accurate allelic expression measurement requires substantial sequencing depth.
  • High-throughput sequencing is a powerful tool for studying regulatory variation and evolution.
  • This approach can reveal evolutionary differences in gene regulation between species.