{"accessLimitation":{"value":"noLimitations","availability":"Available","description":"Access to the resource is not subject to any access limitations and is available to all users without restriction.","uri":"http://vocab.nerc.ac.uk/collection/N07/current/UNRS/"},"authors":[{"familyName":"Cavers","givenName":"S.","organisationName":"UK Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"author","email":"enquiries@ceh.ac.uk","nameIdentifier":"https://orcid.org/0000-0003-2139-9236","fullName":"Cavers, S."},{"familyName":"Wachowiak","givenName":"W.","organisationName":"Adam Mickiewicz University","organisationIdentifier":"https://ror.org/04g6bbq64","role":"author","email":"witwac@amu.edu.pl","nameIdentifier":"https://orcid.org/0000-0003-2898-3523","fullName":"Wachowiak, W."},{"familyName":"Perry","givenName":"A.","organisationName":"UK Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"author","email":"enquiries@ceh.ac.uk","nameIdentifier":"https://orcid.org/0000-0002-7889-7597","fullName":"Perry, A."}],"availability":"Available","boundingBoxes":[{"westBoundLongitude":-18.359,"eastBoundLongitude":24.839,"southBoundLatitude":37.192,"northBoundLatitude":67.115,"bounds":"{\"type\": \"Feature\",      \"properties\": {},      \"geometry\": {        \"type\": \"Polygon\",        \"coordinates\": [[[-18.359, 37.192], [-18.359, 67.115], [24.839, 67.115], [24.839, 37.192], [-18.359, 37.192]]]      }}","coordinates":"[[[-18.359, 37.192], [-18.359, 67.115], [24.839, 67.115], [24.839, 37.192], [-18.359, 37.192]]]"}],"citation":{"authors":["Cavers, S.","Wachowiak, W.","Perry, A."],"bibtex":"https://catalogue.ceh.ac.uk/documents/7ee55609-d6b1-4693-8b36-2bf84fef76c2/citation?format=bib","day":27,"doi":"10.5285/7ee55609-d6b1-4693-8b36-2bf84fef76c2","month":3,"publisher":"NERC Environmental Information Data Centre","resourceTypeGeneral":"dataset","ris":"https://catalogue.ceh.ac.uk/documents/7ee55609-d6b1-4693-8b36-2bf84fef76c2/citation?format=ris","title":"Scots pine single nucleotide polymorphism (SNP) genotypes for Axiom array validation","url":"https://doi.org/10.5285/7ee55609-d6b1-4693-8b36-2bf84fef76c2","year":2020},"custodians":[{"organisationName":"NERC EDS Environmental Information Data Centre","organisationIdentifier":"https://ror.org/04xw4m193","role":"custodian","email":"info@eidc.ac.uk"}],"datasetReferenceDate":{"publicationDate":"2020-03-27","releasedDate":"2020-03-31"},"description":"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.","distributionFormats":[{"name":"Plain text","type":"text/plain","version":"unknown"}],"distributorContacts":[{"organisationName":"NERC EDS Environmental Information Data Centre","organisationIdentifier":"https://ror.org/04xw4m193","role":"distributor","email":"info@eidc.ac.uk"}],"funding":[{"funderName":"Natural Environment Research Council","funderIdentifier":"https://ror.org/02b5d8509","orcid":false,"ror":true}],"id":"7ee55609-d6b1-4693-8b36-2bf84fef76c2","incomingCitationCount":1,"incomingCitations":[{"description":"Perry, A., Wachowiak, W., Downing, A., Talbot, R., & Cavers, S. (2020). Development of a single nucleotide polymorphism array for population genomic studies in four European pine species. Molecular Ecology Resources, 20(6), 1697–1705.","url":"https://doi.org/10.1111/1755-0998.13223"}],"infoLinks":[{"url":"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","type":"OTHER"}],"inspireThemes":[{"theme":"Environmental Monitoring Facilities","uri":"http://inspire.ec.europa.eu/theme/ef"}],"keywordsOther":[{"value":"Natural selection "},{"value":"Speciation "},{"value":"Divergence "},{"value":"Polymorphism "},{"value":"Genotyping "},{"value":"SNPs"},{"value":"Population genomics "},{"value":"Genomic "},{"value":"Micoarray "}],"keywordsTheme":[{"value":"Biodiversity","uri":"http://onto.nerc.ac.uk/CEHMD/topic/2"},{"value":"Environmental survey","uri":"http://onto.nerc.ac.uk/CEHMD/topic/7"}],"licences":[{"value":"This resource is available under the terms of the Open Government Licence","code":"license","uri":"https://eidc.ac.uk/licences/ogl/plain"}],"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.\n\n 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).","metadataDate":"2026-06-29T16:47:46","notGEMINI":false,"onlineResources":[{"url":"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","type":"OTHER"},{"url":"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","type":"OTHER"}],"pointsOfContact":[{"honorificPrefix":"Dr","familyName":"Cavers","givenName":"Stephen","organisationName":"UK Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"pointOfContact","email":"enquiries@ceh.ac.uk","address":{"deliveryPoint":"Bush Estate","city":"Penicuik","administrativeArea":"Midlothian","postalCode":"EH26 0QB","country":"United Kingdom"},"fullName":"Cavers, S.","pointOfContact":"UK Centre for Ecology & Hydrology"}],"publicationDate":"2020-03-27T00:00:00.000Z","publishers":[{"organisationName":"NERC Environmental Information Data Centre","organisationIdentifier":"https://ror.org/04xw4m193","role":"publisher","email":"info@eidc.ac.uk"}],"resourceIdentifiers":[{"code":"https://catalogue.ceh.ac.uk/id/7ee55609-d6b1-4693-8b36-2bf84fef76c2"},{"code":"10.5285/7ee55609-d6b1-4693-8b36-2bf84fef76c2","codeSpace":"doi"}],"resourceType":{"value":"dataset"},"responsibleParties":[{"familyName":"Cavers","givenName":"S.","organisationName":"UK Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"author","email":"enquiries@ceh.ac.uk","nameIdentifier":"https://orcid.org/0000-0003-2139-9236","fullName":"Cavers, S."},{"familyName":"Wachowiak","givenName":"W.","organisationName":"Adam Mickiewicz University","organisationIdentifier":"https://ror.org/04g6bbq64","role":"author","email":"witwac@amu.edu.pl","nameIdentifier":"https://orcid.org/0000-0003-2898-3523","fullName":"Wachowiak, W."},{"familyName":"Perry","givenName":"A.","organisationName":"UK Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"author","email":"enquiries@ceh.ac.uk","nameIdentifier":"https://orcid.org/0000-0002-7889-7597","fullName":"Perry, A."},{"honorificPrefix":"Dr","familyName":"Cavers","givenName":"Stephen","organisationName":"UK Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"pointOfContact","email":"enquiries@ceh.ac.uk","address":{"deliveryPoint":"Bush Estate","city":"Penicuik","administrativeArea":"Midlothian","postalCode":"EH26 0QB","country":"United Kingdom"},"fullName":"Cavers, S.","pointOfContact":"UK Centre for Ecology & Hydrology"},{"organisationName":"NERC EDS Environmental Information Data Centre","organisationIdentifier":"https://ror.org/04xw4m193","role":"custodian","email":"info@eidc.ac.uk"},{"organisationName":"NERC Environmental Information Data Centre","organisationIdentifier":"https://ror.org/04xw4m193","role":"publisher","email":"info@eidc.ac.uk"},{"organisationName":"UK Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"rightsHolder","email":"enquiries@ceh.ac.uk"}],"rightsHolders":[{"organisationName":"UK Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"rightsHolder","email":"enquiries@ceh.ac.uk"}],"spatialReferenceSystems":[{"code":"http://www.opengis.net/def/crs/EPSG/0/4326","title":"WGS 84"}],"spatialRepresentationTypes":["textTable"],"spatialResolutions":[{"distance":"10000","uom":"urn:ogc:def:uom:EPSG::9001"}],"title":"Scots pine single nucleotide polymorphism (SNP) genotypes for Axiom array validation","topicCategories":[{"value":"biota","uri":"http://inspire.ec.europa.eu/metadata-codelist/TopicCategory/biota"}],"topics":["http://onto.nerc.ac.uk/CEHMD/topic/2","http://onto.nerc.ac.uk/CEHMD/topic/7"],"type":"dataset","uri":"https://catalogue.ceh.ac.uk/id/7ee55609-d6b1-4693-8b36-2bf84fef76c2","useConstraints":[{"value":"This resource is available under the terms of the Open Government Licence","code":"license","uri":"https://eidc.ac.uk/licences/ogl/plain"}]}