Metagenomic analyses of the hydrothermal shrimp Rimicaris exoculata cephalothoracic epibiotic community
We use shotgun metagenomics to reconstruct novel Rimicaris exoculata cephalothoracic epibiotic genomes and unravel their potential metabolic functions
Simple
- Title
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Metagenomic analyses of the hydrothermal shrimp Rimicaris exoculata cephalothoracic epibiotic community
- Date (Creation)
- 2014-01-28
- Date (Publication)
- 2018-03-22
- Citation identifier
- FR-330-715-368-00032-DATARMOR_BIOINFO-RIMICARIS
- Citation identifier
- DOI:10.12770/4186eeef-32b1-4ffb-9a40-61a02a3852b7
- Abstract
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We use shotgun metagenomics to reconstruct novel Rimicaris exoculata cephalothoracic epibiotic genomes and unravel their potential metabolic functions
- Credit
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Ifremer - Laboratoire de Microbiologie des Environnements Extrêmes - Projets ABYSS, REMIMA and LabexMer
- Point of contact
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Organisation name Individual name Electronic mail address Role IFREMER
Aube Johanne
Author IFREMER
Cambon-Bonavita Marie-Anne
Author IFREMER
Publisher
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GEMET - INSPIRE themes, version 1.0
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Habitats and biotopes
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Thèmes Sextant
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/Biological Environment/Bioinformatics
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Type de jeux de donnée ODATIS
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/Sequences
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ODATIS aggregation parameters and Essential Variable names
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Bioinformatics
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- Use limitation
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Public access
- Access constraints
- Copyright
- Use constraints
- Copyright
- Spatial representation type
- Grid
- Language
- English
- Character set
- UTF8
- Topic category
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- Oceans
- Begin date
- 2014-01-29
- End date
- 2014-02-03
- Reference system identifier
- EPSG / WGS 84 (EPSG:4326) / 8.6
- Topology level
- Geometry only
- Number of dimensions
- 2
- Dimension name
- Column
- Dimension name
- Row
- Cell geometry
- Area
- Distribution format
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Name Version
- OnLine resource
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Protocol Linkage Name WWW:LINK-1.0-http--metadata-URL
http://dx.doi.org/10.12770/4186eeef-32b1-4ffb-9a40-61a02a3852b7 DOI of the dataset
NETWORK:LINK
/home/ref-bioinfo/ifremer/lmee/REX_Reveillaud WWW:DOWNLOAD-1.0-link--download
https://data-dataref.ifremer.fr/bioinfo/ifremer/lmee/REX_Reveillaud/ Download link
WWW:LINK-1.0-http--publication-URL
http://dx.doi.org/10.17600/14000100 Publication
- Hierarchy level
- Dataset
- Statement
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We collected Rimicaris exoculata specimens using a suction sampler manipulated by the Remote Operated Vehicle (ROV) Victor 6000 on board on the research vessel Pourquoi pas?. Samples were taken from three hydrothermal sites on the Mid Atlantic Ridge: Rainbow during the MoMAR and the Biobaz cruise, TAG and Snake Pit during the BICOSE cruise.
We performed DNA extraction of the six Rimicaris cephalothoracic appendages (2 branchiostegites + 2 scaphognathites + 2 exopodites).
We sheared DNA to 175 bp using a Covaris S-series sonicator and completed metagenomic library construction using the Ovation Ultralow Library DR multiplex system (Nugen) following manufacturer’s instructions. We performed metagenomic sequencing on an Illumina HiSeq 1000 and a NextSeq at the W.M. Keck sequencing facility at the Marine Biological Laboratory. All libraries were paired-end, with a 30 bp overlap, resulting in an average merged read length of 170 bp.
Metadata
- File identifier
- 4186eeef-32b1-4ffb-9a40-61a02a3852b7
- Metadata language
- English
- Character set
- UTF8
- Hierarchy level
- Dataset
- Date stamp
- 2023-07-06T11:56:07.718Z
- Metadata standard name
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ISO 19115:2003/19139 - SEXTANT
- Metadata standard version
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1.0
- Metadata author
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Organisation name Individual name Electronic mail address Role IFREMER
Aube Johanne
Local service desk IFREMER
Cambon-Bonavita Marie-Anne
Local service desk IFREMER
Lamy Jean-Baptiste
Local service desk