Loch Etive Depth Cores Ion Torrent FASTQ Data (NERC Grant NE/L000326/1)
Two sediment depth cores were collected from the floor of Loch Etive, near Oban, Scotland. Slicing was performed in an anaerobic bag. Samples were taken at 0.5 cm increment between 0 - 2 cm, 1 cm increments between 2 - 10 cm, and at either 2 or 5 cm increments thereafter. Samples were transferred to Newcastle University for DNA extraction. A total of 21 samples were extracted for core 1, and 23 samples extracted for core 2.
INSPIRE
Identification
- File identifier
- a0046fac-9c62-30ee-e054-002128a47908 XML
- Resource type
- dataset
Online resource
Resource identifier
- Metadata Language
- English (en)
Encoding
- Format
-
FASTQ file
Projection
Classification of data and services
- Topic category
-
- Geoscientific information
Classification of data and services
Coupled resource
Coupled resource
Classification of data and services
Coupled resource
Coupled resource
Keywords
- GEMET - INSPIRE themes, version 1.0
- BGS Thesaurus of Geosciences
-
-
Uranium
-
NGDC Deposited Data
-
Bacteria
-
Geographic coverage
Temporal reference
Temporal extent
Temporal extent
- Dataset Reference Date ()
- 2020-02-21
Quality and validity
- Lineage
-
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.
Conformity
Conformity
Conformity
Conformity
Conformity
Conformity
- Explanation
-
See the referenced specification
Restrictions on access and use
- Access constraints
- licenceOGL
- Access constraints
- Available under the Open Government Licence subject to the following acknowledgement accompanying the reproduced NERC materials "Contains NERC materials ©NERC [year]"
- Access 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.
- Access constraints
-
Available under the Open Government Licence subject to the following acknowledgement accompanying the reproduced NERC materials "Contains NERC materials ©NERC [year]"
Responsible organization (s)
Contact for the resource
- Organisation name
-
University of Newcastle
-
not available
- Organisation name
-
University of Newcastle
-
not available
Responsible organization (s)
Contact for the resource
- Organisation name
-
University of Newcastle
-
not available
- Organisation name
-
University of Newcastle
-
not available
Metadata information
Contact for the metadata
- Organisation name
-
British Geological Survey
-
enquiries@bgs.ac enquiries@bgs.ac.uk
- Metadata Date
- 2024-04-18
- Metadata Language
- English (en)