Identification

Title

16S rRNA Gene Sequencing of Filtered Groundwater from 8 Boreholes in Cambodia (NERC grant NE/P01304X/1)

Abstract

This dataset represents the raw reads from sequencing the V4 hyper-variable region of the 16S rRNA gene on an Illumina MiSeq platform. The samples are filtered groundwater samples from 8 boreholes from a sandy-dominated site and a clay-dominated site in Cambodia that show arsenic concentrations above the WHO recommended limit, and were collected in May 2019.

Resource type

nonGeographicDataset

Resource locator

https://www.bgs.ac.uk/services/ngdc/accessions/index.html#item130306

name: Data

function: download

Unique resource identifier

code

http://data.bgs.ac.uk/id/dataHolding/13607536

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

Groundwater

NGDC Deposited Data

Arsenic

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

East bounding longitude

North bounding latitude

South bounding latitude

Extent

Extent group

authority code

title

reference date

date type

creation

effective date

1979

code identifying the extent

KAMPUCHEA [id=548000]

Extent group

authority code

title

reference date

date type

creation

effective date

1979

code identifying the extent

KANDAL [id=548780]

Temporal reference

Temporal extent

Begin position

2019-05-06

End position

2019-05-12

Dataset reference date

date type

creation

effective date

2019-09-26

Frequency of update

notApplicable

Quality and validity

Lineage

Groundwater (500 mL) was collected in sterile plastic bottles (Corning), and filtered through a sterile 0.2 um nitrocellulose filter (Whatman). The filters were placed in DNA/RNA Shield Collection and Lysis Tubes (ZymoResearch) and homogenised using a Terralyzer (ZymoResearch) and transported to the UK. DNA was extracted from the samples, along with 3 negative controls, using the ZymoBIOMICS DNA Kit (ZymoResearch), according to the manufacturer's recommendations. A small volume (2 uL) from the extracted DNA was used to amplify the V4 hyper-variable region of the 16S rRNA gene by PCR, using a barcoded 515F and 806R primers, and the FastStart High Fidelity PCR System (Roche Diagnostics). The barcoded PCR products were purified and normalised to ~20 ng each, using the SequalPrep Normalization Kit (Fisher Scientific), pooled and sequenced on an Illumina MiSeq platform using V2 chemistry.

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 files

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

School of Earth and Environmental Sciences

organisation name

University of Manchester

full postal address

Manchester

M13 9PL

email address

not available

responsible party role

principalInvestigator

Responsible party

contact position

School of Earth and Environmental Sciences

organisation name

University of Manchester

full postal address

Williamson Building

Manchester

M13 9PL

email address

not available

responsible party role

originator

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

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

2024-04-11

Metadata language