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Related Experiment Video

Updated: Jul 28, 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 method to generate capture baits for targeted sequencing.

Balaji Sundararaman^1,2, Alisa O Vershinina³, Samantha Hershauer^1,2

¹Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

Nucleic Acids Research

|June 1, 2023

Summary

This summary is machine-generated.

This study introduces Circular Nucleic acid Enrichment Reagent (CNER), a novel method for creating DNA probes. CNER significantly improves targeted high-throughput sequencing for challenging samples like ancient DNA.

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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

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Published on: August 4, 2016

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

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Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

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Published on: September 3, 2009

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Hybridization capture enables cost-effective targeted high-throughput sequencing.
It is crucial for analyzing low-target-content, fragmented DNA from ancient, environmental, or forensic samples.
Existing targeted approaches may fail with compromised DNA quality.

Purpose of the Study:

To develop a novel DNA bait synthesis method for hybridization capture.
To introduce the Circular Nucleic acid Enrichment Reagent (CNER) approach.
To evaluate CNER's efficiency compared to commercial methods for ancient DNA sequencing.

Main Methods:

CNER utilizes rolling-circle amplification followed by restriction digestion to produce hybridization probes.
Probes were designed for 23,771 single nucleotide polymorphism sites in the horse genome.
CNER capture efficiency was compared against a commercial method using ten ancient horse DNA libraries.

Main Results:

CNER successfully generated hybridization probes for targeted sequencing.
CNER captured significantly more targets (90.5%) compared to a commercial approach (66.5%).
CNER achieved greater mean sequencing depth per sample.

Conclusions:

CNER is an effective and efficient method for DNA bait synthesis in hybridization capture.
CNER outperforms commercial approaches for targeted sequencing of ancient DNA.
This method advances genomic analysis of challenging DNA samples.