• Catalogue PIGMA
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Metabarcoding of Coastal Ecosystems

A total number of 277 water samples were collected during distinct oceanographic cruises or at fixed stations across coastal systems of France and Senegal. The seawater samples were progressively filtered onto size-fractionated filters (representing micro, nano and pico-plankton). Metabarcoding of the V4 domain of the Eukaryotic 18S rDNA region was carried out to characterize the genetic diversity of the sampled communities. Genomic DNA was extracted following the DNA extraction kit Nucleospin Plant II (Macherey-Nagel) and the V4 markers were amplified with a taq polymerase (Phusion High-Fidelity PCR Master Mix with GC Buffer). Sequencing was performed by the Genotoul sequencing platform (get.genotoul.fr) with the Illumina MISeq method (2x250 bp). The present dataset gathers the different results issued from sequencing. This dataset was submitted to sequence cleaning, filtering, taxonomic assignment and OTU clustering, which resulted in a final dataset also presented.

Simple

Date (Creation)
2016-04-18T00:00:00
Identifier
FR-330-715-368-00032-DATARMOR_BIOINFO_POHEM
Identifier
DOI:10.12770/16bc16ef-588a-47e2-803e-03b4acb85dca
Credit
Projet POHEM - Laboratoire Dyneco PELAGOS and Station Biologique de Roscoff
Author
  IFREMER - Ramond Pierre
Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané , Brest , France
02 98 22 42 60
Author
  IFREMER - Siano Raffaele
Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané , Brest , France
02 98 22 42 04
02 98 22 45 48
Author
  IFREMER - Sourisseau Marc
Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané , Brest , France
02 98 22 43 61
02 98 22 45 48
Publisher
  IFREMER - SISMER
Thèmes Sextant
  • /Biological Environment/Bioinformatics
Keywords
  • Metabarcoding
  • Protist
  • Coastal Ecosystem
ODATIS aggregation parameters and Essential Variable names
  • Bioinformatics
Use limitation
Data under Licence ouverte / Open licence : http://www.etalab.gouv.fr/pages/licence-ouverte-open-licence-5899923.html
Access constraints
Copyright
Use constraints
License
Spatial representation type
grid Grid
Metadata language
English
Character set
utf8 UTF8
Topic category
  • Oceans
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Begin date
2009-01-07
End date
2015-11-25
Reference system identifier
EPSG / WGS 84 (EPSG:4326) / 8.6
Distribution format
  • ( )

OnLine resource
DOI of the dataset ( DOI )

DOI of the dataset

OnLine resource
Download link ( WWW:DOWNLOAD )

Download link

OnLine resource
/home/ref-bioinfo-public/ifremer-controlled/dyneco/POHEM ( NETWORK:LINK )
Hierarchy level
Dataset
Statement

A link to the dataset can be sent upon request.

The link will access a two folder repository :

- [data] contains: [dna-sequence-raw] inculding raw sequencing data of each sample for the reverse and forward V4 markers (R1 & R2); [otu-table] which is our final table (after sequence cleaning, filtering, taxonomic assignment with PR² (Guillou et al., 2013) and OTU clustering with swarm2 (Mahé et al., 2015).

- [operation] contains diverse operations carried out by the sequencing platform (see inside) and a merging of reverse and forward sequences [sequence-merging]

File identifier
16bc16ef-588a-47e2-803e-03b4acb85dca XML
Metadata language
English
Character set
UTF8
Hierarchy level
Dataset
Date stamp
2025-05-15T21:29:00.994353Z
Metadata standard name
ISO 19115-3 - SEXTANT
Metadata standard version
1.0
Author
  IFREMER - Ramond Pierre
Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané , Brest , France
02 98 22 42 60
Point of contact
  IFREMER - Raffaele Siano
Author
  IFREMER - Sourisseau Marc
 
 

Overviews

overview

Spatial extent

N
S
E
W
thumbnail


Keywords

ODATIS aggregation parameters and Essential Variable names
Bioinformatics
Thèmes Sextant
/Biological Environment/Bioinformatics

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