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Updated: Sep 24, 2025

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

A 3'-end capture sequencing method for high-throughput targeted gene expression profiling.

Eric de Bony^1,2, Fien Gysens¹, Nurten Yigit^1,2

¹OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium.

Biotechnology Journal

|May 10, 2022

Summary

This summary is machine-generated.

Shallow 3'-end RNA sequencing can now profile low-abundance genes, including long noncoding RNAs (lncRNAs), cost-effectively. This new 3'-end RNA capture sequencing method enriches target genes over 200-fold for accurate expression profiling.

Keywords:

RNA-sequencing abundance capture-sequencing coverage probes transcriptomics

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Last Updated: Sep 24, 2025

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

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Published on: August 4, 2016

3' End Sequencing Library Preparation with A-seq2

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

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

Published on: October 5, 2018

Area of Science:

Molecular biology
Genomics
Biotechnology

Background:

Shallow 3 -end RNA sequencing is used for large-scale perturbation screens.
Standard workflows struggle with low-abundance transcripts like lncRNAs.
Targeted gene expression profiling is crucial for disease biology and drug discovery.

Purpose of the Study:

To develop a cost-effective method for targeted gene expression profiling.
To improve the quantification of low-abundance transcripts using shallow sequencing.
To enable accurate profiling of selected gene panels across numerous samples.

Main Methods:

Combined 3 -end library preparation with 3 -end hybrid capture probes and shallow RNA sequencing.
Designed a capture probe set for over 100 mRNA and lncRNA targets.
Applied the workflow to 360 samples.

Main Results:

Achieved over 200-fold enrichment of target gene abundance compared to standard 3 -end RNA sequencing.
Maintained relative intergene and intersample abundances.
Demonstrated accurate targeted gene expression profiling at shallow sequencing depths.

Conclusions:

3 -end RNA capture sequencing offers a cost-effective solution for targeted gene expression analysis.
The method enhances the detection of low-abundance transcripts.
Enables accurate molecular phenotyping in large-scale studies.