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Data Publisher for Earth & Environmental Science

De Vargas, Colomban; Tara Oceans Expedition, Participants; Tara Oceans Consortium, Coordinators (2015): List of size fractionated eukaryotic plankton community samples and associated metadata (Database W1). PANGAEA, https://doi.org/10.1594/PANGAEA.843017, Supplement to: De Vargas, Colomban; Audic, Stephane; Henry, Nicolas; Decelle, Johan; Mahe, Jean-Claude; Logares, Ramiro; Lara, Enrique; Berney, Cédric; Le Bescot, Noan; Probert, Ian; Carmichael, Margaux; Poulain, Julie; Romac, Sarah; Colin, Sébastien; Aury, Jean-Marc; Bittner, Lucie; Chaffron, Samuel; Dunthorn, Micah; Engelen, Stefan; Flegontova, Olga; Horák, Aleš; Jaillon, Olivier; Lima-Mendez, Gipsi; Lukes, Julius; Malviya, Shruti; Morard, Raphael; Mulot, Matthieu; Scalco, Eleonora; Siano, Raffaele; Zingone, Adriana; Picheral, Marc; Searson, Sarah; Kandels-Lewis, Stefanie; Acinas, Silvia G; Gorsky, Gabriel; Grimsley, Nigel; Hingamp, Pascal; Iudicone, Daniele; Not, Fabrice; Ogata, Hiroyuki; Sieracki, Michael; Speich, Sabrina; Stemmann, Lars; Sunagawa, Shinichi; Wincker, Patrick; Karsenti, Eric (2015): First Tara Oceans V9 rDNA metabarcoding dataset. zenodo, https://doi.org/10.5281/zenodo.15600

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Abstract:
The present data set provides an Excel file in a zip archive. The file lists 334 samples of size fractionated eukaryotic plankton community with a suite of associated metadata (Database W1). Note that if most samples represented the piconano- (0.8-5 µm, 73 samples), nano- (5-20 µm, 74 samples), micro- (20-180 µm, 70 samples), and meso- (180-2000 µm, 76 samples) planktonic size fractions, some represented different organismal size-fractions: 0.2-3 µm (1 sample), 0.8-20 µm (6 samples), 0.8 µm - infinity (33 samples), and 3-20 µm (1 sample). The table contains the following fields: a unique sample sequence identifier; the sampling station identifier; the Tara Oceans sample identifier (TARA_xxxxxxxxxx); an INDSC accession number allowing to retrieve raw sequence data for the major nucleotide databases (short read archives at EBI, NCBI or DDBJ); the depth of sampling (Subsurface - SUR or Deep Chlorophyll Maximum - DCM); the targeted size range; the sequences template (either DNA or WGA/DNA if DNA extracted from the filters was Whole Genome Amplified); the latitude of the sampling event (decimal degrees); the longitude of the sampling event (decimal degrees); the time and date of the sampling event; the device used to collect the sample; the logsheet event corresponding to the sampling event ; the volume of water sampled (liters). Then follows information on the cleaning bioinformatics pipeline shown on Figure W2 of the supplementary litterature publication: the number of merged pairs present in the raw sequence file; the number of those sequences matching both primers; the number of sequences after quality-check filtering; the number of sequences after chimera removal; and finally the number of sequences after selecting only barcodes present in at least three copies in total and in at least two samples. Finally, are given for each sequence sample: the number of distinct sequences (metabarcodes); the number of OTUs; the average number of barcode per OTU; the Shannon diversity index based on barcodes for each sample (URL of W4 dataset in PANGAEA); and the Shannon diversity index based on each OTU (URL of W5 dataset in PANGAEA).
Other version:
De Vargas, Colomban: First Tara Oceans V9 rDNA metabarcoding dataset. http://taraoceans.sb-roscoff.fr/EukDiv
Project(s):
Fondation Tara Expeditions (FondTara)
Tara Oceans Expedition (TOE-2009-2013)
Comment:
Excel file compressed in a zip archive
Size:
51.0 kBytes

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