High-quality RNA extraction from copepods for Next Generation Sequencing: A comparative study

Asai, S; Ianora, A; Lauritano, C; Lindeque, PK; Carotenuto, Y. 2015 High-quality RNA extraction from copepods for Next Generation Sequencing: A comparative study. Marine Genomics, 24. 115-118. 10.1016/j.margen.2014.12.004

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Official URL: http://dx.doi.org/10.1016/j.margen.2014.12.004

Abstract/Summary

Despite the ecological importance of copepods, few Next Generation Sequencing studies (NGS) have been performed on small crustaceans, and a standard method for RNA extraction is lacking. In this study, we compared three commonly-used methods: TRIzol®, Aurum Total RNA Mini Kit and Qiagen RNeasy Micro Kit, in combination with preservation reagents TRIzol® or RNAlater®, to obtain high-quality and quantity of RNA from copepods for NGS. Total RNA was extracted from the copepods Calanus helgolandicus, Centropages typicus and Temora stylifera and its quantity and quality were evaluated using NanoDrop, agarose gel electrophoresis and Agilent Bioanalyzer. Our results demonstrate that preservation of copepods in RNAlater® and extraction with Qiagen RNeasy Micro Kit were the optimal isolation method for high-quality and quantity of RNA for NGS studies of C. helgolandicus. Intriguingly, C. helgolandicus 28S rRNA is formed by two subunits that separate after heat-denaturation and migrate along with 18S rRNA. This unique property of protostome RNA has never been reported in copepods. Overall, our comparative study on RNA extraction protocols will help increase gene expression studies on copepods using high-throughput applications, such as RNA-Seq and microarrays.

Item Type: Publication - Article
Additional Keywords: Copepods; Total RNA extraction; NGS; RIN; Transcriptome
Subjects: Ecology and Environment
Marine Sciences
Divisions: Plymouth Marine Laboratory > Science Areas > Marine Life Support Systems
Depositing User: Pennie Lindeque
Date made live: 05 Feb 2016 15:13
Last Modified: 06 Jun 2017 16:15
URI: http://plymsea.ac.uk/id/eprint/6777

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