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Optimization of preservation and storage time of sponge tissues to obtain quality mRNA for next-generation sequencing

Authors

  • ANA RIESGO,

    1. Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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  • ALICIA R. PÉREZ-PORRO,

    1. Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
    2. Center for Advanced Studies of Blanes, c/Accés a la Cala St. Francesc, 14, 17300 Blanes, Girona, Spain
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  • SUSANA CARMONA,

    1. Harvard Social Cognitive Neuroscience Lab, 52 Oxford Street, Cambridge, MA 02138, USA
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  • SALLY P. LEYS,

    1. Department of Biological Sciences, University of Alberta, T6G 2E9, Edmonton, Alberta, Canada
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  • GONZALO GIRIBET

    1. Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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Ana Riesgo, Fax: +1 617 495 5667; E-mail: ariesgo@oeb.harvard.edu

Abstract

Transcriptome sequencing with next-generation sequencing technologies has the potential for addressing many long-standing questions about the biology of sponges. Transcriptome sequence quality depends on good cDNA libraries, which requires high-quality mRNA. Standard protocols for preserving and isolating mRNA often require optimization for unusual tissue types. Our aim was assessing the efficiency of two preservation modes, (i) flash freezing with liquid nitrogen (LN2) and (ii) immersion in RNAlater, for the recovery of high-quality mRNA from sponge tissues. We also tested whether the long-term storage of samples at −80 °C affects the quantity and quality of mRNA. We extracted mRNA from nine sponge species and analysed the quantity and quality (A260/230 and A260/280 ratios) of mRNA according to preservation method, storage time, and taxonomy. The quantity and quality of mRNA depended significantly on the preservation method used (LN2 outperforming RNAlater), the sponge species, and the interaction between them. When the preservation was analysed in combination with either storage time or species, the quantity and A260/230 ratio were both significantly higher for LN2-preserved samples. Interestingly, individual comparisons for each preservation method over time indicated that both methods performed equally efficiently during the first month, but RNAlater lost efficiency in storage times longer than 2 months compared with flash-frozen samples. In summary, we find that for long-term preservation of samples, flash freezing is the preferred method. If LN2 is not available, RNAlater can be used, but mRNA extraction during the first month of storage is advised.

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