TITLE: Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition
AUTHORS: Adriana  Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, Patrick Wincker

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<div class = "text-blocks"><div class = "text-block">The protocols in this collection are from the Alberti A., et al manuscript (Alberti A. 2017, Scientific Data). </div><div class = "text-block"><span>These protocols provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, </span><a href="http://www.ebi.ac.uk/ena" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">www.ebi.ac.uk/ena</span></a><span>). This collection complements other efforts to provide a full description of experiments and open science resources generated from the </span><span style = "font-style:italic;">Tara </span><span>Oceans project, further extending their value for the study of the world’s planktonic ecosystems.'</span></div><div class = "text-block">From the Methods section:</div><div class = "text-block">'The generation of information-rich data from marine plankton samples presents unique challenges that are inherent to the particular sampling conditions at sea and the wide spectrum of organisms included in that environment. All processing steps, including biomass collection, sample preservation, nucleic acids extractions and sequencing library preparation, are critical and require specific protocols and robust methods in order to ensure comparability of results and limit potential biases.</div><div class = "text-block"><span>Our methods were either developed specifically for </span><span style = "font-style:italic;">Tara</span><span> Oceans samples or carefully selected among existing ones in order to meet the requirements of our sequencing strategy and to produce optimized datasets for downstream bioinformatics analyses, as for example the production of overlapping reads from metagenomics libraries to facilitate assembly. They are presented in five sub-sections, starting with a brief description of how samples were handled between the research vessel and the processing laboratories (</span><a href="https://www.protocols.io/view/handling-of-genomics-samples-qwfdxbn" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">protocol 1</span></a><a href="https://www.protocols.io/view/handling-of-genomics-samples-qwfdxbn" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;:;">)</span></a><span>. </span><a href="https://www.protocols.io/view/nucleic-acids-preparations-qwgdxbw" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">Protocol 2</span></a><span> reports on DNA and RNA extractions procedures for -omics analyses, including the generation of amplified genomic DNA from uncultured isolated unicellular eukaryotes. The generation of 18S and 16S rRNA amplicons from DNA of specific size-fractions is described in </span><a href="https://www.protocols.io/view/18s-and-16s-rrna-genes-amplicon-generation-for-euk-qwhdxb6" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">protocol 3</span></a><span> and Illumina libraries preparation in </span><a href="https://www.protocols.io/view/sequencing-library-preparation-qwidxce" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">protocol 4</span></a><span>. Sequencing procedures and post-sequencing data processing are described in </span><a href="https://www.protocols.io/view/sequencing-and-data-quality-control-qwjdxcn" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">protocol 5</span></a><span>. For details on the onboard sampling protocols, see </span><a href="https://www.nature.com/articles/sdata201523" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">Pesant </span></a><a href="https://www.nature.com/articles/sdata201523" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-style:italic;">et al</span></a><span style = "font-style:italic;">.'</span><span></span></div></div>

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