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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
 
Citation proposal
Aube Johanne (IFREMER) - Cambon-Bonavita Marie-Anne (IFREMER) (2018) . Metagenomic analyses of the hydrothermal shrimp Rimicaris exoculata cephalothoracic epibiotic community. IFREMER https://services.mspdata.eu:/geonetwork/srv/api/records/4186eeef-32b1-4ffb-9a40-61a02a3852b7

Simple

Date ( Creation )
2013-08-11
Date ( Publication )
2018-03-22
Identifier
FR-330-715-368-00032-DATARMOR_BIOINFO-RIMICARIS
Identifier
DOI:10.12770/4186eeef-32b1-4ffb-9a40-61a02a3852b7
Credit
Ifremer - Laboratoire de Microbiologie des Environnements Extrêmes - Projets ABYSS, REMIMA and LabexMer

  Author

IFREMER - Aube Johanne  

  Author

IFREMER - Cambon-Bonavita Marie-Anne  
Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané Brest France

  02 98 22 47 56  
  02 98 22 47 57 

  Publisher

IFREMER -  

GEMET - INSPIRE themes, version 1.0 ( Theme )
  • Habitats and biotopes
Thèmes Sextant ( Theme )
  • /Biological Environment/Bioinformatics
Use limitation
Public access
Access constraints
Copyright
Use constraints
Copyright
Other constraints
Spatial representation type
Grid
Metadata language
English
Character set
UTF8
Topic category
  • Oceans
N
S
E
W


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
  • ( )

OnLine resource
DOI of the dataset  

DOI of the dataset

OnLine resource
/home/ref-bioinfo/ifremer/lmee/REX_Reveillaud  
OnLine resource
Download link  

Download link

Hierarchy level
Dataset
Statement

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   XML
Metadata language
English
Character set
UTF8
Hierarchy level
Dataset
Date stamp
2021-08-11T16:58:21
Metadata standard name
ISO 19115:2003/19139 - SEXTANT
Metadata standard version
1.0

  Point of contact

IFREMER - Aube Johanne  

  Point of contact

IFREMER - Cambon-Bonavita Marie-Anne  
Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané Brest France

  02 98 22 47 56  
  02 98 22 47 57 

  Point of contact

IFREMER - Lamy Jean-Baptiste  
Station de La Tremblade - Ronce Les Bains - 17390 La Tremblade La Tremblade France

  05 46 76 26 13  
 
 

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