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Ravenglass Depth Cores Ion Torrent FASTQ Data (NERC Grant NE/L000326/1)

Two sediment depth cores were collected from the River Esk estuary during low tide near the town of Ravenglass, UK. Cores were collected by the University of Manchester. Cores were sliced at 1 cm intervals from 0 - 10 cm, and at 2 cm intervals thereafter. Slicing was performed in an anaerobic bag. Samples were transferred to Newcastle University for DNA extraction. A total of 19 samples were extracted for core 1, and 18 samples extracted for core 2.
 
Citation proposal
. Ravenglass Depth Cores Ion Torrent FASTQ Data (NERC Grant NE/L000326/1). https://metadata.bgs.ac.uk/geonetwork/srv/api/records/9f8e367b-d26f-3fa5-e054-002128a47908

Simple

Date ( Creation )
2020
Identifier
http://data.bgs.ac.uk/id/dataHolding/13607591

  Originator

University of Newcastle - Peter Leary (Bioinformatics Support Unit )  
Leech Building, Faculty of Medical Sciences, Framlington Place Newcastle NE2 4HH

  Principal investigator

University of Newcastle - Dr Neil Gray (Sch of Natural & Environmental Sciences )  
Agriculture Building Newcastle NE1 7RU

  Distributor

British Geological Survey - Enquiries  

  Point of contact

British Geological Survey - Enquiries  

Maintenance and update frequency
notApplicable notApplicable
GEMET - INSPIRE themes
  • Geology
BGS Thesaurus of Geosciences
  • Core samples , Bacteria , Uranium
Keywords
  • NERC_DDC
Access constraints
otherRestrictions Other restrictions
Use constraints
otherRestrictions Other restrictions
Other constraints
The copyright of materials derived from the British Geological Survey's work is vested in the Natural Environment Research Council [NERC]. No part of this work may be reproduced or transmitted in any form or by any means, or stored in a retrieval system of any nature, without the prior permission of the copyright holder, via the BGS Intellectual Property Rights Manager. Use by customers of information provided by the BGS, is at the customer's own risk. In view of the disparate sources of information at BGS's disposal, including such material donated to BGS, that BGS accepts in good faith as being accurate, the Natural Environment Research Council (NERC) gives no warranty, expressed or implied, as to the quality or accuracy of the information supplied, or to the information's suitability for any use. NERC/BGS accepts no liability whatever in respect of loss, damage, injury or other occurence however caused.
Other constraints
Either: (i) the dataset is made freely available, e.g. via the Internet, for a restricted category of use (e.g. educational use only); or (ii) the dataset has not been formally approved by BGS for access and use by external clients under licence, but its use may be permitted under alternative formal arrangements; or (iii) the dataset contains 3rd party data or information obtained by BGS under terms and conditions that must be consulted in order to determine the permitted usage of the dataset. Refer to the BGS staff member responsible for the creation of the dataset if further advice is required. He / she should be familiar with the composition of the dataset, particularly with regard to 3rd party IPR contained in it, and any resultant use restrictions. This staff member should revert to the IPR Section (ipr@bgs.ac.uk ) for advice, should the position not be clear.
Spatial representation type
textTable Text, table
Metadata language
English English
Topic category
  • Geoscientific information
Geographic identifier
Ravenglass [id=1458961]

 

Date ( Revision )
2002

N
S
E
W


Reference system identifier
OGP / GEOG

 

Date ( Revision )
2005

Distribution format
  • fastq ()

  Distributor

British Geological Survey - Enquiries  

OnLine resource
https://www.bgs.ac.uk/services/ngdc/accessions/index.html#item132965  
Hierarchy level
dataset Dataset
Other
dataset

Conformance result

Date ( Publication )
2011
Explanation
See the referenced specification
Pass
false

Conformance result

Date ( Publication )
2010-12-08
Explanation
See http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2010:323:0011:0102:EN:PDF
Pass
false
Statement
DNA was extracted using FastDNA SPIN Kit for Soil. PCR using the 515F and 926R primers targeting the V4-V5 region of the 16S rRNA gene. Amplicon length was 481 bp. PCRs were 25 uL reactions with 22 uL of MegaMix Blue, 1uL of forward and 1 uL of reverse primer at 100 pM concentration, and 1 uL of 1:10 diluted template DNA. Initial denaturation was 95C for 5 minutes, followed by 30 cycles of 95C for 1 minute, 55C for 1 minutes, 72C for 1 minute, and a final elongation step of 72C for 10 minutes. Each depth sample was run in triplicate and pooled. Pooled amplicons were cleaned using Agencourt AMPure XP. PCR amplicons were quantified via Qubit 3.0 fluorometer and a total dilution factor was calculated for each sample, diluting each sample to 1000. Equimolar samples were pooled into a final library. Sequencing was performed on the Ion Torrent PGM on a 316 chip.

gmd:MD_Metadata

File identifier
9f8e367b-d26f-3fa5-e054-002128a47908   XML
Metadata language
English English
Hierarchy level
dataset Dataset
Date stamp
2021-01-19
Metadata standard name
UK GEMINI
Metadata standard version
2.3

  Point of contact

British Geological Survey  
Environmental Science Centre,Keyworth NOTTINGHAM NOTTINGHAMSHIRE NG12 5GG United Kingdom

  +44 115 936 3100  
Dataset URI
http://data.bgs.ac.uk/id/dataHolding/13607591
 
 

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