Title

Metabarcoding of Coastal Ecosystems

Date (Creation)

2016-04-18T00:00:00

Citation identifier

FR-330-715-368-00032-DATARMOR_BIOINFO_POHEM

Citation identifier

DOI:10.12770/16bc16ef-588a-47e2-803e-03b4acb85dca

Abstract

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.

Credit

Projet POHEM - Laboratoire Dyneco PELAGOS and Station Biologique de Roscoff

Point of contact

Organisation name	Individual name	Electronic mail address	Role
IFREMER	Ramond Pierre	Pierre.Ramond@ifremer.fr	Author
IFREMER	Siano Raffaele	Raffaele.Siano@ifremer.fr	Author
IFREMER	Sourisseau Marc	Marc.Sourisseau@ifremer.fr	Author
IFREMER - SISMER		sismer@ifremer.fr	Publisher

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

Language

English

Character set

UTF8

Topic category

• Oceans

Begin date

2009-01-07

End date

2015-11-25

Reference system identifier

EPSG / WGS 84 (EPSG:4326) / 8.6

Distribution format

Name	Version

OnLine resource

Protocol	Linkage	Name
WWW:LINK-1.0-http--metadata-URL	https://doi.org/10.12770/16bc16ef-588a-47e2-803e-03b4acb85dca	DOI of the dataset

OnLine resource

Protocol	Linkage	Name
WWW:DOWNLOAD-1.0-link--download	https://data-dataref.ifremer.fr/bioinfo/ifremer/dyneco/POHEM/	Download link
NETWORK:LINK	/home/ref-bioinfo-public/ifremer-controlled/dyneco/POHEM

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]

Metadata

File identifier

16bc16ef-588a-47e2-803e-03b4acb85dca

Metadata language

English

Character set

UTF8

Hierarchy level

Dataset

Date stamp

2024-08-28T13:02:03.115Z

Metadata standard name

ISO 19115:2003/19139 - SEXTANT

Metadata standard version

1.0

Metadata author

Organisation name	Individual name	Electronic mail address	Role
IFREMER	Ramond Pierre	Pierre.Ramond@ifremer.fr	Author
IFREMER	Raffaele Siano	raffaele.siano@ifremer.fr	Local service desk
IFREMER	Sourisseau Marc	marc.sourisseau@ifremer.fr	Author