Identification info

Metadata Language

English (en)

Character set

utf8

Dataset Reference Date ()

2020-03-27

Identifier

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

Identifier

doi: / 10.5285/7ee55609-d6b1-4693-8b36-2bf84fef76c2

Other citation details

Cavers, S., Wachowiak, W., Perry, A. (2020). Scots pine single nucleotide polymorphism (SNP) genotypes for Axiom array validation. NERC Environmental Information Data Centre 10.5285/7ee55609-d6b1-4693-8b36-2bf84fef76c2

GEMET - INSPIRE themes, version 1.0 ()

• Environmental Monitoring Facilities

Keywords

• Biodiversity
• Environmental survey
• Pinus sylvestris, Pinus mugo, Pinus uliginosa, Pinus uncinata
• Genomic
• SNPs
• Population genomics
• Micoarray
• Genotyping
• Polymorphism
• Divergence
• Speciation
• Natural selection

Limitations on Public Access

otherRestrictions

Other constraints

no limitations

Use constraints

otherRestrictions

Other constraints

This resource is available under the terms of the Open Government Licence

Use constraints

otherRestrictions

Other constraints

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

Spatial representation type

textTable

Distance

10000  urn:ogc:def:uom:EPSG::9001

Topic category

• Biota

 

Code

WGS 84

Distribution Information

Data format

• text ()

 

Quality Scope

dataset

Other

dataset

Statement

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).

Metadata

File identifier

7ee55609-d6b1-4693-8b36-2bf84fef76c2 XML

Metadata Language

English (en)

Character set

ISO/IEC 8859-1 (also known as Latin 1)

Resource type

dataset

Hierarchy level name

dataset

Metadata Date

2021-06-25T18:40:46

Metadata standard name

UK GEMINI

Metadata standard version

2.3