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

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

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Asai, Sneha Ianora, Adrianna Lauritano, Chiara Lindeque, Penelope K. Carotenuto, Ylenia
Description	Author Affiliation: Asai S ( Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy. Electronic address: sneha.asai@gmail.com.); Ianora A ( Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.); Lauritano C ( Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.); Lindeque PK ( Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.); Carotenuto Y ( Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy. Electronic address: ylenia@szn.it.)
Abstract	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.
File Format	HTM / HTML
ISSN	18747787
Journal	Marine Genomics
Volume Number	24 Pt 1
e-ISSN	18767478
Language	English
Publisher	Elsevier
Publisher Date	2015-12-01
Publisher Place	Netherlands
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Discipline Genetics Discipline Biology Copepoda Genetics High-throughput Nucleotide Sequencing Methods Specimen Handling Animals Rna, Ribosomal, 18s Species Specificity Journal Article Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Genetics Aquatic Science

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