Year: 2017
Type: data-paper
Abstract: A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we 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, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.
Source: Scientific Data
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, Frédérick Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Mark Wessner, Genoscope Technical Team, Pascal Bazire, Odette Beluche, Laurie Bertrand, Marielle Besnard-Gonnet, Isabelle Bordelais, Magali Boutard, Maria Dubois, Corinne Dumont, Evelyne Ettedgui, Patricia Fernandez, Espérance Garcia, Nathalie Giordanenco Aiach, Thomas Guerin, Chadia Hamon, Elodie Brun, Sandrine Lebled, Patricia Lenoble, Claudine Louesse, Eric Mahieu, Barbara Mairey, Nathalie Martins, Catherine Megret, Claire Milani, Jacqueline Muanga, Céline Orvain, Emilie Payen, Peggy Perroud, Emmanuelle Petit, Dominique Robert, Murielle Ronsin, Benoit Vacherie, 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, Silvia G. Acinas, Peer Bork, Emmanuel Boss, Chris Bowler, Colomban De Vargas, Michael Follows, Gabriel Gorsky, Nigel Grimsley, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels-Lewis, Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Stéphane Pesant, Jeroen Raes, Christian Sardet, Michael E. Sieracki, Sabrina Speich, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa, Patrick Wincker, Stéphane Pesant, Eric Karsenti, Patrick Wincker
Institutions: Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Genoscope, Institut de biologie François Jacob, Centre National de la Recherche Scientifique, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Université Pierre-et-Marie-Curie, Consejo Superior de Investigaciones Científicas, Institut de Ciències del Mar, Génomique Métabolique du Genoscope, Inserm, Université Paris Sciences et Lettres, École Normale Supérieure - PSL, Institut de Biologie de l'École Normale Supérieure, University of Chile, European Bioinformatics Institute, Sorbonne Université, Biologie Intégrative des Organismes Marins, Observatoire Océanologique de Banyuls-sur-Mer, European Molecular Biology Laboratory, European Molecular Biology Laboratory, Kyoto University, Kyoto University Institute for Chemical Research, Bigelow Laboratory for Ocean Sciences, U.S. National Science Foundation, The Ohio State University, University of Michigan, University of Arizona, Max Delbrück Center, Heidelberg University, University of Würzburg, University of Maine, Massachusetts Institute of Technology, Laboratoire d’Océanographie de Villefranche, Observatoire Océanologique de Villefranche-sur-Mer, Université de Toulon, Aix-Marseille Université, Institut Méditerranéen d’Océanologie, Institut de Recherche pour le Développement, Stazione Zoologica Anton Dohrn, University of Bremen, VIB-KU Leuven Center for Microbiology, KU Leuven, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Laboratoire de Météorologie Dynamique, Institut Universitaire Européen de la Mer, Institute of Microbiology
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
SDG: Life below water
Open Access status: gold
Estimated APC paid: $1,132
Funders: National Science Foundation, European Molecular Biology Laboratory, European Commission, Agence Nationale de la Recherche, Fondation pour la Recherche sur la Biodiversite, Centre National de la Recherche Scientifique, Ministerio de Ciencia e Innovación, Fondation Veolia Environnement, Région Bretagne, Biotechnology and Biological Sciences Research Council, Japan Society for the Promotion of Science
Awards: G1554707310, G1580281708, A holistic ecosystemic investigation of marine giruses, virophages and their eukaryotic hosts, G1748285061, G2435021273, G2579310621, Bacterial dormancy, bacterivory, and bacterioplankton diversity in the ocean, G4742956268, G667825618, Building a global metagenomics portal ('MGportal') to handle next generation sequencing data and associated metadata, Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques, Diversity of marine protists: single cell genomics and imaging for Tara Oceans, G705061367, MRI: Acquisition of genome sequencers for Bigelow Laboratory for Ocean Sciences, G7240651115, G7999552054, G8114080009, G916719672, Marine Microbial Biodiversity, Bioinformatics and Biotechnology
OpenAlex ID: W2740316488