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Sci Data. 2017 Aug 1;4:170093. doi: 10.1038/sdata.2017.93.

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.

Author information

1
CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.
2
CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.
3
Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.
4
Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain.
5
CNRS, UMR 8030, Evry CP5706, France.
6
Université d'Evry, UMR 8030, Evry CP5706, France.
7
FONDAP Center for Genome Regulation, Moneda 1375, Santiago 8320000, Chile.
8
Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Libano Macul, Santiago 5524, Chile.
9
Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France.
10
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK.
11
CNRS UMR 7232, BIOM, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.
12
Sorbonne Universités Paris 06, OOB UPMC, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.
13
Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.
14
Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.
15
for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
16
Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA.
17
National Science Foundation, Arlington, Virginia 22230, USA.
18
Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio 43210, USA.
19
Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA.
20
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
21
University of Arizona, Tucson, Arizona 85721, USA.
22
Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, Arizona 85719, USA.
23
MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Str. 8, Bremen 28359, Germany.
24
PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Leobener Str. 8, Bremen 28359, Germany.
25
Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, 181 Chemin du Lazaret, Villefranche-sur-mer F-06230, France.

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.

PMID:
28763055
PMCID:
PMC5538240
DOI:
10.1038/sdata.2017.93
[Indexed for MEDLINE]
Free PMC Article

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