BGS Hosted Metadata
Scots pine single nucleotide polymorphism (SNP) genotypes for Axiom array validation
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
Simple
- Date (Publication)
- 2020-03-27
- Citation identifier
- https://catalogue.ceh.ac.uk/id/7ee55609-d6b1-4693-8b36-2bf84fef76c2
- Citation identifier
- doi: / 10.5285/7ee55609-d6b1-4693-8b36-2bf84fef76c2
- Other citation details
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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
- Point of contact
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Organisation name Individual name Electronic mail address Role UK Centre for Ecology & Hydrology Cavers, S. Author Adam Mickiewicz University Wachowiak, W. Author UK Centre for Ecology & Hydrology Perry, A. Author UK Centre for Ecology & Hydrology Cavers, S.
Point of contact NERC EDS Environmental Information Data Centre Custodian NERC Environmental Information Data Centre Publisher UK Centre for Ecology & Hydrology Owner
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GEMET - INSPIRE themes, version 1.0
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Environmental Monitoring Facilities
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- Access constraints
- Other restrictions
- Other constraints
- no limitations
- Use constraints
- Other restrictions
- Use constraints
- Other restrictions
- Other constraints
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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
- Text, table
- Distance
- 10000 urn:ogc:def:uom:EPSG::9001
- Language
- English
- Character set
- UTF8
- Topic category
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- Biota
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- Unique resource identifier
- WGS 84
- Distribution format
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Name Version text
- Distributor contact
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre
Distributor
- OnLine resource
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Protocol Linkage Name https://data-package.ceh.ac.uk/data/7ee55609-d6b1-4693-8b36-2bf84fef76c2 Download the data
- OnLine resource
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Protocol Linkage Name https://data-package.ceh.ac.uk/sd/7ee55609-d6b1-4693-8b36-2bf84fef76c2.zip Supporting information
- Hierarchy level
- Dataset
- Other
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dataset
Conformance result
- Title
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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
- Statement
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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
- Character set
- 8859 Part 1
- Hierarchy level
- Dataset
- Hierarchy level name
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dataset
- Date stamp
- 2025-03-21T13:21:09
- Metadata standard name
- UK GEMINI
- Metadata standard version
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2.3
- Metadata author
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre Point of contact
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