Identification

Title

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

Abstract

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.

Resource type

dataset

Resource locator

https://www.bgs.ac.uk/services/ngdc/accessions/index.html#item133105

name: Data

function: download

Unique resource identifier

code

http://data.bgs.ac.uk/id/dataHolding/13607594

codeSpace

Dataset language

eng

Spatial reference system

code identifying the spatial reference system

Classification of spatial data and services

Topic category

geoscientificInformation

Keywords

Keyword set

keyword value

originating controlled vocabulary

title

reference date

date type

publication

effective date

2008-06-01

Keyword set

keyword value

Uranium

NGDC Deposited Data

Bacteria

originating controlled vocabulary

title

reference date

date type

revision

effective date

2022

Keyword set

keyword value

Keyword set

keyword value

NERC_DDC

Geographic location

West bounding longitude

-5.2400

East bounding longitude

-5.2400

North bounding latitude

56.4400

South bounding latitude

56.4400

Extent

Extent group

authority code

title

reference date

date type

revision

effective date

2002

code identifying the extent

Loch Etive [id=1344178]

Temporal reference

Temporal extent

Begin position

2017-06-01

End position

2017-06-14

Dataset reference date

date type

creation

effective date

2020-02-21

Frequency of update

notApplicable

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 report

specification

title

reference date

date type

publication

effective date

2011

degree

false

explanation

See the referenced specification

Conformity report

specification

title

reference date

date type

publication

effective date

2010-12-08

degree

false

explanation

See http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2010:323:0011:0102:EN:PDF

Data format

name of format

FASTQ file

version of format

Constraints related to access and use

Constraint set

Limitations on public access

Constraint set

Limitations on public access

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.

Responsible organisations

Responsible party

contact position

Bioinformatics Support Unit

organisation name

University of Newcastle

full postal address

Leech Building, Faculty of Medical Sciences, Framlington Place

Newcastle

NE2 4HH

email address

not available

responsible party role

originator

Responsible party

contact position

Bioinformatics Support Unit

organisation name

University of Newcastle

full postal address

Leech Building, Faculty of Medical Sciences, Framlington Place

Newcastle

NE2 4HH

email address

not available

responsible party role

principalInvestigator

Responsible party

organisation name

British Geological Survey

email address

not available

responsible party role

distributor

Responsible party

organisation name

British Geological Survey

email address

not available

responsible party role

originator

Responsible party

organisation name

British Geological Survey

email address

not available

responsible party role

pointOfContact

Metadata on metadata

Metadata point of contact

organisation name

British Geological Survey

full postal address

Environmental Science Centre,Keyworth

NOTTINGHAM

NG12 5GG

United Kingdom

telephone number

+44 115 936 3100

email address

enquiries@bgs.ac.uk

responsible party role

pointOfContact

Metadata date

2025-04-06

Metadata language