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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 microarray-based...

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Updated: May 11, 2026

AQRNA-seq for Quantifying Small RNAs

AQRNA-seq for Quantifying Small RNAs

Published on: February 2, 2024

eQTL Mapping Using RNA-seq Data.

Wei Sun¹, Yijuan Hu

¹Department of Biostatistics, Department of Genetics, Carolina Center of Genome Science, UNC Chapel Hill, Chapel Hill, NC 27599, USA.

Statistics in Biosciences

|May 14, 2013

Summary

This summary is machine-generated.

RNA sequencing (RNA-seq) advances gene expression studies by enabling allele-specific expression (ASE) analysis and detailed RNA-isoform profiling. This review covers current methods for eQTL mapping using ASE and discusses future directions for isoform-specific eQTL studies.

Keywords:

Allele-specific gene expression (ASE)Gene expression quantitative trait locus (eQTL)RNA isoform RNA-seq

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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Area of Science:

Genomics
Transcriptomics
Bioinformatics

Background:

RNA sequencing (RNA-seq) is increasingly adopted for genome-wide transcription abundance analysis, surpassing traditional gene expression microarrays.
RNA-seq offers novel capabilities for gene expression Quantitative Trait Locus (eQTL) studies, including allele-specific expression (ASE) and detailed RNA-isoform expression analysis.

Purpose of the Study:

To review current methodologies for eQTL mapping utilizing allele-specific expression (ASE) data derived from RNA-seq.
To explore existing research on RNA-isoform expression analysis using RNA-seq data.
To identify research gaps and outline future directions for isoform-specific eQTL mapping.

Main Methods:

Review of existing literature on eQTL mapping methods.
Analysis of RNA-seq data features relevant to eQTL studies (ASE and isoform expression).
Comparative assessment of current RNA-isoform expression studies and their relation to isoform-specific eQTL mapping.

Main Results:

RNA-seq provides allele-specific expression (ASE) information, a feature absent in microarrays, enhancing eQTL studies.
RNA-seq generates rich data for comprehensive RNA-isoform expression analysis.
Current isoform expression studies using RNA-seq have gaps when compared to the requirements for isoform-specific eQTL mapping.

Conclusions:

Allele-specific expression (ASE) analysis using RNA-seq is a powerful tool for eQTL studies.
Further research is needed to bridge the gap between current RNA-isoform expression analysis and isoform-specific eQTL mapping.
Future directions include developing and refining methods for isoform-specific eQTL mapping to fully leverage RNA-seq data.