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

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.

Date (Creation): 2019-09-26

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

Point of contact

Organisation name	Individual name	Electronic mail address	Role
University of Manchester	Prof Jonathan Lloyd	not available	Principal investigator
University of Manchester	Dr Naji Bassil	not available	Originator
British Geological Survey	Enquiries	not available	Distributor
British Geological Survey	Enquiries	not available	Point of contact

Maintenance and update frequency: notApplicable

GEMET - INSPIRE themes, version 1.0

Geology

BGS Thesaurus of Geosciences

Groundwater
NGDC Deposited Data
Arsenic

dataCentre

NGDC Deposited Data

Keywords

NERC_DDC

Access constraints: Other restrictions

Other constraints: licenceOGL

Other constraints: Available under the Open Government Licence subject to the following acknowledgement accompanying the reproduced NERC materials "Contains NERC materials ©NERC [year]"

Use constraints: 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: Available under the Open Government Licence subject to the following acknowledgement accompanying the reproduced NERC materials "Contains NERC materials ©NERC [year]"

Language: English

Topic category

Geoscientific information

Geographic identifier: KAMPUCHEA [id=548000]
British Geological Survey Gazetteer: Geographical hierarchy from Geosaurus 1979 creation

Geographic identifier: KANDAL [id=548780]
British Geological Survey Gazetteer: Geographical hierarchy from Geosaurus 1979 creation

Begin date: 2019-05-06

End date: 2019-05-12

Reference System Information

No information provided.

Distribution format

Name	Version
.fastq files

Distributor contact

Organisation name	Individual name	Electronic mail address	Role
British Geological Survey	Enquiries	not available	Distributor

OnLine resource

Protocol	Linkage	Name
	https://www.bgs.ac.uk/services/ngdc/accessions/index.html#item130306	Data

Hierarchy level: Non geographic dataset

Other: non geographic dataset

Conformance result

Title: INSPIRE Implementing rules laying down technical arrangements for the interoperability and harmonisation of Geology

Date (Publication): 2011

Explanation: See the referenced specification

Pass: No

Conformance result

Title: Commission Regulation (EU) No 1089/2010 of 23 November 2010 implementing Directive 2007/2/EC of the European Parliament and of the Council as regards interoperability of spatial data sets and services

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: No

Statement: 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.