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
dataset
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
https://catalogue.ceh.ac.uk/id/7ee55609-d6b1-4693-8b36-2bf84fef76c2
doi:
eng
biota
Environmental Monitoring Facilities
publication
2008-06-01
creation
2012-10-29
Natural selection
Speciation
Divergence
Polymorphism
Genotyping
SNPs
Population genomics
Genomic
Micoarray
-18.359
24.839
67.115
37.192
publication
2020-03-27
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).
publication
2010-12-08
text
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
UK Centre for Ecology & Hydrology
author
Adam Mickiewicz University
author
UK Centre for Ecology & Hydrology
author
UK Centre for Ecology & Hydrology
pointOfContact
NERC EDS Environmental Information Data Centre
custodian
NERC Environmental Information Data Centre
publisher
UK Centre for Ecology & Hydrology
owner
Environmental Information Data Centre
Lancaster Environment Centre, Library Avenue, Bailrigg
Lancaster
LA1 4AP
UK
pointOfContact
2023-02-09T11:09:36