2025-06-11
ENA first public
ERC000024
ENA-CHECKLIST
Ifremer
INSDC center name
public
INSDC status
Production of targeted PCR from 10 ng of DNA material. The aim is to generate amplified targeted regions indexed with secondary identifiers or BID = Barcoded Identifiers. In the protocol, the region of interest is amplified using PCR Forward and Reverse primers flanked by sequences of 8 bases, called "BID" (the name has been developed at Genoscope to differentiate from other MIDs = Molecular Identifiers already in use at the time). To date, 18 different BID sequences have been tested, 12 of which have been selected. The amplicons generated will be then normalized and pooled by up to 12 (amplicons carrying different BID sequences). Illumina libraries will be prepared by Genoscope on each pool of BIDed amplicons and then Illumina sequenced
LIBRARY_CONSTRUCTION_PROTOCOL
ERS24933543
SRA accession
sam_LINKS-zooplankton_S9-80um
Submitter Id
COX1
TARGETED_LOCI
neritic epipelagic zone biome
broad-scale environmental context
SeBiMER
broker name
PDG-ODE-DYNECO-PELAGOS
collected_by
IFREMER
collecting institution
2021-10-22
collection date
Aurore Regaudie de Gioux
collector name
seawater metagenome
common name
-23
m
depth
seawater
environmental medium
water
environmental package
yes
environmental_sample
location,depth,filter/mesh size
experimental factor
France
geographic location (country and/or sea)
not applicable
m
geographic location (elevation)
6.21
DD
geographic location (latitude)
-53.03
DD
geographic location (longitude)
Station S09
geographic location (region and locality)
metagenome
investigation type
Filtered seawater from French Guiana coastal waters
isolation_source
coastal sea water
local environmental context
CGAGTCGT
multiplex identifiers
seawater metagenome
organism
F: GGWACWGGWTGAACWGTWTAYCCYCC  /  R: TAIACYTCIGGRTGICCRAARAAYCA
pcr primers
LINKS_zooplankton
project name
FOF Oceanographic Cruise: LINKS (2021), environmental DNA from seawater, station S09, seawater sampled plankton net with a 80 um mesh.
sample_description
S9-80um
sample_name
seawater metagenome
scientific_name
Sequencing by synthesis (Illumina)
sequencing method
COX1
target gene
not applicable
target subfragment
Seawater eDNA metabarcording of COX1 station S09, seawater sampled plankton net with a 80 um mesh.
title