eDNA

This technical platform has been set up to allow ecologists to perform large-scale analysis of environmental DNA via a metabarcoding approach. DNA metabarcoding refers to high throughput DNA-based identification of multiple species from environmental DNA. The main applications consist in diet analysis from feces, in biodiversity assessment using soil or water samples, and in palaeo-environment reconstruction using lake sediments and permafrost samples.

The eDNA platform is composed of three pre-PCR extraction rooms dedicated to feces, soil, and ancient DNA, and to several post-PCR rooms dedicated to the purification and the titration of PCR products. The next generation sequencing on Illumina platforms (HiSeq or MiSeq) is outsourced. The eDNA platform also possesses all the equipment that can be transported and installed in the field to allow DNA extraction straight after the sampling.

The eDNA platform can provide support to:

(I) Design the experiment according to the scientfic goal, and ensure data quality given the technical contraints

(ii) perform large-scale DNA extractions

(iii) perform large-scale DNA amplifications

(iv) outsource DNA sequencing to a company having developped protocols ensuring high quality amplicon sequencing from eDNA samples

(v) analyze raw sequences to produce a contengency table that will be analyzed later on by the prosecutor

(vi) help discussing the scientific results with regards to the possible pitfalls of the metabarcoding approach

 
Citation proposal
. eDNA. https://services.mspdata.eu:/geonetwork/srv/api/records/6c173c29-ec47-4324-bfb2-e1d6bc92566d

Simple

Date ( Creation )
2016-06-01
Unique resource identifier
Maintenance and update frequency
As needed
theme.anaeeThes.rdf ( Theme )
  • microbial biomass , microbial diversity , soil worms , AnaEE-France , soil biomass , soil fauna , ecosystem management , pathogen
GEMET - INSPIRE themes, version 1.0 INSPIRE themes ( Theme )
  • Environmental monitoring facilities
AnaEE-France Locations ( Place )
  • France
Use limitation
See AnaEE-France charters.
Access constraints
Intellectual property rights
Use constraints
Intellectual property rights
Denominator
50000
Metadata language
English
Character set
UTF8
Topic category
  • Structure
Description
France
N
S
E
W


Unique resource identifier
Distribution format
  • ( )

OnLine resource
web site  
OnLine resource
site metabracoding  
OnLine resource
https://git.metabarcoding.org/obitools/obitools/wikis/home  
Hierarchy level
Dataset

Conformance result

Date ( Publication )
Explanation
Statement
no information

Metadata

File identifier
6c173c29-ec47-4324-bfb2-e1d6bc92566d   XML
Metadata language
English
Character set
UTF8
Hierarchy level
Dataset
Date stamp
2018-07-12T13:01:38
Metadata standard name
ISO 19115:2003/19139
Metadata standard version
1.0
 
 

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