Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

RNA-seq

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...

You might also read

Related Articles

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

Sort by

Same author

Phylogenomics yields new systematic and taxonomical insights for Lissotriton newts, a genus with a strong legacy of introgressive hybridization.

Molecular phylogenetics and evolution·2025

Same author

Widespread Adaptive Introgression of Major Histocompatibility Complex Genes across Vertebrate Hybrid Zones.

Molecular biology and evolution·2024

Same author

Limited evidence for genetic differentiation or adaptation in two amphibian species across replicated rural-urban gradients.

Evolutionary applications·2024

Same author

The genomic response to urbanization in the damselfly <i>Ischnura elegans</i>.

Evolutionary applications·2023

Same author

Water and ion diffusion in partially-water saturated compacted kaolinite: Role played by vapor-phase diffusion in water mobility.

Journal of contaminant hydrology·2022

Same author

Sexual selection drives the evolution of male wing interference patterns.

Proceedings. Biological sciences·2019

Search research articles

Related Experiment Video

Updated: May 7, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Accuracy of allele frequency estimation using pooled RNA-Seq.

M Konczal¹, P Koteja, M T Stuglik

¹Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.

Molecular Ecology Resources

|October 15, 2013

Summary

Pooled RNA-Seq accurately estimates allele frequencies in nonmodel organisms, offering a cost-effective alternative for population genetics. Accounting for gene expression variation improves accuracy, making it comparable to pooled genome resequencing.

Keywords:

RNA-Seq accuracy estimation bank vole pool transcriptome

More Related Videos

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Related Experiment Videos

Last Updated: May 7, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Area of Science:

Population genetics
Genomics
Transcriptomics

Background:

RNA-Sequencing (RNA-Seq) enables genome-wide variation analysis in nonmodel organisms via de novo transcriptome assembly.
High costs of library preparation limit population genetic studies in nonmodel species.
Sample pooling presents a cost-effective strategy for population-level analyses.

Purpose of the Study:

To evaluate the accuracy of pooled RNA-Seq in estimating true allele frequencies.
To compare pooled RNA-Seq accuracy with individually barcoded RNA-Seq.
To identify factors influencing the accuracy of pooled RNA-Seq allele frequency estimation.

Main Methods:

Analyzed liver transcriptomes of 10 bank voles, sequencing each sample individually and as a pool.
Mapped RNA-Seq reads to a de novo assembled reference transcriptome.
Compared allele frequencies from pooled samples to high-quality genotypes from individual samples (23,682 SNPs).

Main Results:

Pooled RNA-Seq allele frequency estimates showed high correlation with true frequencies.
Mean relative estimation error was 21%, independent of expression level.
Minor allele frequency and interindividual gene expression variation impacted estimation accuracy.

Conclusions:

Pooled RNA-Seq provides accurate allele frequency estimation, comparable to pooled genome resequencing.
Assessing and accounting for interindividual gene expression variation is crucial for optimizing accuracy.
This method is valuable for population genetic analyses of nonmodel organisms with cost constraints.