Identification

Title

Scots pine single nucleotide polymorphism (SNP) genotypes for Axiom array validation

Abstract

The dataset contains genotypes for samples used to validate a 50K single nucleotide polymorphism (SNP, DNA mutation) Axiom array for Scots pine (Pinus sylvestris) and closely related members of the Pinus mugo complex. Full details about this dataset can be found at https://doi.org/10.5285/7ee55609-d6b1-4693-8b36-2bf84fef76c2

Resource type

dataset

Resource locator

https://data-package.ceh.ac.uk/data/7ee55609-d6b1-4693-8b36-2bf84fef76c2

name: Download the data

description: Download a copy of this data

function: download

https://data-package.ceh.ac.uk/sd/7ee55609-d6b1-4693-8b36-2bf84fef76c2.zip

name: Supporting information

description: Supporting information available to assist in re-use of this dataset

function: information

Unique resource identifier

code

https://catalogue.ceh.ac.uk/id/7ee55609-d6b1-4693-8b36-2bf84fef76c2

codeSpace

doi:

Dataset language

eng

Spatial reference system

code identifying the spatial reference system

Classification of spatial data and services

Topic category

biota

Keywords

Keyword set

keyword value

Environmental Monitoring Facilities

originating controlled vocabulary

title

GEMET - INSPIRE themes, version 1.0

reference date

date type

publication

effective date

2008-06-01

Keyword set

keyword value

originating controlled vocabulary

title

Wikidata

reference date

date type

creation

effective date

2012-10-29

Keyword set

keyword value

Natural selection

Speciation

Divergence

Polymorphism

Genotyping

SNPs

Population genomics

Genomic

Micoarray

Geographic location

West bounding longitude

-18.359

East bounding longitude

24.839

North bounding latitude

67.115

South bounding latitude

37.192

Temporal reference

Temporal extent

Begin position

End position

Dataset reference date

date type

publication

effective date

2020-03-27

Frequency of update

Quality and validity

Lineage

Samples & Validation of the array was carried out using a subset of 87 samples, which included four species of pine (Pinus sylvestris: SY; P. mugo: MU; P. uncinata: UN; P. uliginosa: UL). DNA was extracted from needles using a Qiagen DNeasy 96 kit following the manufacturer’s instructions. Needles were dried on silica gel prior to extraction and DNA was quantified using a Qubit spectrophotometer to ensure a minimum standardized concentration of 35ng/µl. The quality of genomic DNA was also checked visually for fragmentation on 1% agarose gel. Genotyping was done at Edinburgh Genomics following DNA amplification, fragmentation, chip hybridisation, single-base extension through DNA ligation and signal amplification performed according to the Affymetrix Axiom® Assay protocol. Genotyping was performed in 384-well format on a GeneTitan according to the manufacturer’s procedure. Genotype calls were performed using Axiom Analysis Suite software as recommended by the manufacturer (ThermoFisher). Samples were assigned to an analysis group based on their call rate (CR) and dish QC (DQC: a metric provided by ThermoFisher which is generated by measuring signals at multiple sites in the genome known not to vary among individuals), using the following thresholds: DQC 'high' ≥ 0.82; DQC 'low' < 0.82; CR 'high' ≥ 96; CR 'low' < 96. Analyses: 1) DQC high + CR high; 2) DQC high + CR low; 3) DQC low + CR low. High quality samples (N=529), with high CR and DQC, were used to set thresholds for allele calls. Posteriors for allele calls were subsequently used as priors for analyses 2 (N = 753) and 3 (N = 251).

Conformity

Conformity report

specification

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

reference date

date type

publication

effective date

2010-12-08

degree

explanation

Data format

name of format

text

version of format

Constraints related to access and use

Constraint set

Limitations on public access

Constraint set

Limitations on public access

Constraint set

Limitations on public access

If you reuse this data, you should cite: Cavers, S., Wachowiak, W., Perry, A. (2020). Scots pine single nucleotide polymorphism (SNP) genotypes for Axiom array validation. NERC Environmental Information Data Centre https://doi.org/10.5285/7ee55609-d6b1-4693-8b36-2bf84fef76c2

Responsible organisations

Responsible party

organisation name

UK Centre for Ecology & Hydrology

email address

enquiries@ceh.ac.uk

responsible party role

author

Responsible party

organisation name

Adam Mickiewicz University

email address

enquiries@ceh.ac.uk

responsible party role

author

Responsible party

organisation name

UK Centre for Ecology & Hydrology

email address

enquiries@ceh.ac.uk

responsible party role

author

Responsible party

organisation name

UK Centre for Ecology & Hydrology

email address

enquiries@ceh.ac.uk

responsible party role

pointOfContact

Responsible party

organisation name

NERC EDS Environmental Information Data Centre

email address

enquiries@ceh.ac.uk

responsible party role

custodian

Responsible party

organisation name

NERC Environmental Information Data Centre

email address

enquiries@ceh.ac.uk

responsible party role

publisher

Responsible party

organisation name

UK Centre for Ecology & Hydrology

email address

enquiries@ceh.ac.uk

responsible party role

owner

Metadata on metadata

Metadata point of contact

organisation name

Environmental Information Data Centre

full postal address

Lancaster Environment Centre, Library Avenue, Bailrigg

Lancaster

LA1 4AP

UK

email address

info@eidc.ac.uk

responsible party role

pointOfContact

Metadata date

2023-02-09T11:09:36

Metadata language

eng