Metatranscriptomic sequences from Alexandrium minutum blooms sampled in situ in the bay of Brest (France) between 2013 and 2015
RNA sequencing of blooms of the toxic dinoflagellate Alexandium minutum. We sequenced three consecutive blooms (2013, 2014, 2015) at a single site (Daoulas) and multiple other bloom from all around the Bay of Brest (SPX samples), Sillon des Anglais, Penzé river, and one sample (Roz) near Daoulas.
Data access Chemin d'accès |
/home/ref-bioinfo/ifremer/dyneco/daoulex
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Date(s) Date(s) |
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Author(s) Auteur(s) |
Metegnier Gabriel
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ECOLE
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Quere Julien ( IFREMER ) Le Gac Mickael ( IFREMER ) |
Contact(s) Contact(s) |
IFREMER
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Source Source |
Ifremer - Dyneco - Laboratoire d'Ecologie Pélagique - Daoulex project |
Lineage Généalogie |
Sample collection and RNA preparation (see details in Metegnier et al., (a,b), submitted) During three consecutive summers (2013, 2014 and 2015), temporal sampling was conducted in the bay of Brest at a single site (48.350543, -4.292507). When the water temperature reached 15°C during spring, a weekly survey of A. minutum densities was performed by the national phytoplankton network (REPHY). When A. minutum densities reached 10 000 cells.L-1 and until densities dropped below this threshold in two consecutive samples, the microphytoplanktonic community was sampled twice a week. A "spatial" sampling of 9 sites (SP1 to SP9, respectively situated at 48°20,192' - 4°22,086'; 48°21,007' - 4°21,091'; 48°21,269' - 4°19,536'; 48°21,218' - 4°16,699'; 48°19,351' - 4°15,577'; 48°18,559' - 4°14,565'; 48°17,749' - 4°12,423'; 48°16,660' - 4°16,882'; 48°18,269' - 4°17,486') situated across the bay of Brest was conducted on June, 14th 2014, four hours around high tide (2 hours before to 2 hours after high tide). Opportunistically, 3 blooms were sampled, one in the Penzé estuary (on the 01/07/2015; 48.644633, -3.950772), one at the Sillon Des Anglais (on the 06/07/2015; 48.299141, -4.288425) and one called 'roz', near our temporal sampling site (on the 08/07/2014). As quickly as possible after the sampling, water was filtered (20 µm) using a peristaltic pump and the filters were frozen into liquid nitrogen and stored at -80°C until RNA extraction. For all samples (Daoulex 2013, 2014, 2015). To prevent RNA degradation during filter thawing, RNA Later Ice® was added before thawing for samples collected in 2013, or samples were directly frozen with RNA Later® in 2014 and 2015. Filters were ultra-sonicated on ice (Bioblock Scientific, Vibra-cell 75115) for 10 seconds at 20% intensity. RNA was extracted following the Quiagen Rneasy Plus Mini Kit® recommendations and library prepared with the Illumina Truseq mRNA V2 kit®. Samples were sequenced at Get-PlaGe France Genomics sequencing platform (Toulouse, France) on Illumina HiSeq 2000/2500 2*100 pb (2013, 2014 and Spatial samples; Multiplex 10) and on HiSeq 3000 2*150 pb for 2015 samples (Multiplex 24). |
Constraints Contraintes |
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Spatial informations Informations géographiques |
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Citation proposal Proposition de citation
Metegnier Gabriel , Quere Julien , Le Gac Mickael (2015).Metatranscriptomic sequences from Alexandrium minutum blooms sampled in situ in the bay of Brest (France) between 2013 and 2015.IFREMER
http://dx.doi.org/10.12770/9d4131da-b33b-429b-9cdd-e7325b06f7d8