{"help":"Return the metadata of a dataset (package) and its resources. :param id: the id or name of the dataset :type id: string","success":true,"result":[{"id":"fc94421f-4e29-46a8-9d45-d54527e06a09","name":"data-development-single-nucleotide-polymorphism-snp-panel-determination-environmental","title":"Data from: Development of Single Nucleotide Polymorphism (SNP) Panel for determination of environmental influence on genome for wild Columbia River redband trout (Oncorhynchus mykiss gairdnerii) in Southwest Idaho streams","author":"Alexander P. Wooding, Shawn R. Narum and Devaleena S. Pradhan","author_email":"devaleenapradhan@isu.edu","maintainer":"RCDS Data Repository","maintainer_email":"rcds-web@uidaho.edu","license_title":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/","notes":"\u003Cp\u003EDNA were derived from fin tissue samples taken from individual trout captured from Little Jacks Creek, Big Jacks Creek , and Duncan Creek of the Owyhee mountains and Keithly Creek and Upper Mann Creek in the Hitt mountains of Western Idaho, United States. Fin tissues were collected from individual trout from each stream during monthly sampling events in June through October 2020.\u003C\/p\u003E\n\u003Cp\u003E\u003Cstrong\u003EDNA Extraction\u003C\/strong\u003E: Extraction of DNA from caudal fin tissues were performed using Quick-DNA Miniprep Plus purification kits (Zymo Research Inc.\u00a9). Small sections of fin tissue (\u2264 25 mg) were collected from each sample. This was mixed with a digesting solution comprised of ultra-pure water, solid tissue buffer (Zymo Research Inc.\u00a9) and proteinase K. All tissues were digested in sealed microcentrifuge tubes for at minimum 3 h at 55\u00b0C in a water bath. We then aliquoted 100 \u00b5L of digestion supernatant and combined with 200 \u00b5L of genomic binding buffer (Zymo Research Inc.\u00a9). DNA was eluted in 50, 75, and 100 \u00b5L of elution buffer to determine which volume provided sufficient DNA concentration for genotyping. After it was determined all quantities produced suitable concentrations, going forward, 50 \u00b5L of elution buffer used.\u003C\/p\u003E\n\u003Cp\u003E\u003Cstrong\u003EGenotyping\u003C\/strong\u003E: Following extraction, genotyping-in-thousands sequencing took place at the Hagerman National Fish Hatchery\u2019s genetics research facility with the assistance of the Columbia River Intertribal Fish Commission (CRTFC). Genotyping protocols were as described in Campbell et al. (2015) and summarized below. First, samples were prepared for amplification via PCR by combining DNA extracts with a Qiagen Plus multiplex master mix and a species-specific pooled primer mix. This step added the Illumina sequencing primer sites to amplicons. Following the creation of the PCR cocktail, thermocycling was conducted for amplification. Amplified samples were then diluted 20-fold. Diluted samples were transferred to new 96-well PCR plates where two genetic indexes and barcodes provides a unique set of tagging primers to each well and plate. Tagged plates then underwent a second PCR step. After the second PCR, all DNA were transferred to Charm Biotech normalization plates where DNA was bound to wells, washed, and finally eluted. After normalization, all DNA was pooled together and a purification step using magnetized beads in two steps to selectively remove fragments of DNA that are both too large and too small for sequencing. Following purification, each plate was quantified via qPCR using Life Technologies QuantStudio 6 Flex Instrument (Life Technologies). Finally, sequencing was performed using an Illumina HiSeq 1500 instrument.\u003C\/p\u003E\n\u003Cp\u003E\u003Cstrong\u003EAncillary peer-reviewed manuscripts\u003C\/strong\u003E:\u003Cbr \/\u003E\n\u003Cem\u003EGenotyping protocols\u003C\/em\u003E\u003Cbr \/\u003E\n Campbell NR, Harmon SA, Narum SR. 2015. Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing. Mol Ecol Resour, 15: 855-867. \u003Ca href=\u0022https:\/\/doi.org\/10.1111\/1755-0998.12357\u0022\u003Ehttps:\/\/doi.org\/10.1111\/1755-0998.12357\u003C\/a\u003E\u003Cbr \/\u003E\n\u003Cem\u003ESNP loci reference\u003C\/em\u003E\u003Cbr \/\u003E\nCollins EE, Hargrove JS, Delomas TA, Narum SR. 2020. Distribution of genetic variation underlying adult migration timing in steelhead of the Columbia River basin. Ecology and Evolution, 10(17): 9486-9502. \u003Ca href=\u0022https:\/\/doi.org\/10.1002\/ece3.6641\u0022\u003Ehttps:\/\/doi.org\/10.1002\/ece3.6641\u003C\/a\u003E\u003C\/p\u003E\n\u003Cp\u003E\u003Cstrong\u003EData Use\u003C\/strong\u003E:\u003Cbr \/\u003E\n\u003Cem\u003ELicense\u003C\/em\u003E: CC-BY 4.0 (\u003Ca href=\u0022https:\/\/creativecommons.org\/licenses\/by\/4.0\/\u0022\u003Ehttps:\/\/creativecommons.org\/licenses\/by\/4.0\/\u003C\/a\u003E)\u003Cbr \/\u003E\n\u003Cem\u003ERecommended Citation\u003C\/em\u003E: Wooding AP, Narum SR, Pradhan DS. 2022. Data from: Development of Single Nucleotide Polymorphism (SNP) Panel for determination of environmental influence on genome for wild Columbia River redband trout (Oncorhynchus mykiss gairdnerii) in Southwest Idaho streams (0.1) [Data set]. Zenodo. \u003Ca href=\u0022https:\/\/doi.org\/10.5281\/zenodo.7055582\u0022\u003Ehttps:\/\/doi.org\/10.5281\/zenodo.7055582\u003C\/a\u003E\u003C\/p\u003E\n","url":"https:\/\/dkan.nkn.uidaho.edu\/dataset\/data-development-single-nucleotide-polymorphism-snp-panel-determination-environmental","state":"Active","log_message":"Edited by awchild.","private":true,"revision_timestamp":"Thu, 08\/31\/2023 - 12:57","metadata_created":"Fri, 09\/09\/2022 - 12:26","metadata_modified":"Thu, 08\/31\/2023 - 12:57","creator_user_id":"6cc16f2c-77c2-4d12-ac06-56bbb86b535b","type":"Dataset","resources":[{"id":"a644a61e-93c6-497f-a4eb-eb804f634291","revision_id":"","url":"https:\/\/doi.org\/10.5281\/zenodo.7055582","description":"","format":"html","state":"Active","revision_timestamp":"Fri, 09\/09\/2022 - 12:27","name":"Data Access Via Zenodo | Data from: Development of Single Nucleotide Polymorphism (SNP) Panel for determination of environmental influence on genome for wild Columbia River redband trout (Oncorhynchus mykiss gairdnerii) in Southwest Idaho streams","mimetype":"html","size":"","created":"Fri, 09\/09\/2022 - 12:27","resource_group_id":"ea4b940c-347f-440a-ba90-23b6bb01560f","last_modified":"Date changed Fri, 09\/09\/2022 - 12:27"}],"tags":[{"id":"3bbad4f9-7651-4bf2-aacd-d11b259f3642","vocabulary_id":"2","name":"Oncorhynchus mykiss gairdneri"},{"id":"36a2c71f-ca58-468c-8c5d-ea3b9e8510c8","vocabulary_id":"2","name":"Redband Trout"},{"id":"9d10045c-9469-4162-99d1-4a4bf8a3c1f0","vocabulary_id":"2","name":"genomics"},{"id":"df18780b-824a-4fe0-994b-3f26204982db","vocabulary_id":"2","name":"SNP"},{"id":"c5976db1-9d4c-41ca-a7a6-a71824fc64c3","vocabulary_id":"2","name":"single-nucleotide polymorphism"},{"id":"7268fffa-e4c5-417c-b5d5-fa1451ad1e9b","vocabulary_id":"2","name":"genome"}],"groups":[{"description":"\u003Cp\u003EIdaho State University, a Carnegie-classified doctoral research and teaching institution founded in 1901, attracts students from around the world to its Idaho campuses. At the main campus in Pocatello, and at locations in Meridian, Idaho Falls and Twin Falls, ISU offers access to high-quality education in more than 250 programs.\u003C\/p\u003E\n\u003Cp\u003ELearn more at \u003Ca href=\u0022https:\/\/www.isu.edu\u0022\u003Ehttps:\/\/www.isu.edu\u003C\/a\u003E\u003C\/p\u003E\n","id":"ea4b940c-347f-440a-ba90-23b6bb01560f","image_display_url":"https:\/\/dkan.nkn.uidaho.edu\/sites\/default\/files\/ISU-black-transbkgrd.png","title":"Idaho State University","name":"group\/idaho-state-university"},{"description":"\u003Cp\u003EThe primary objective of Idaho EPSCoR is to stimulate research in niche areas that can become fully competitive in the disciplinary and multidisciplinary research programs of the National Science Foundation and other relevant agencies. Idaho EPSCoR provides support for sustainable increases in Research and Development capacity and advances science and engineering capabilities within the state. \u003C\/p\u003E\n\u003Cp\u003EVisit them at \u003Ca href=\u0022https:\/\/www.idahoepscor.org\u0022\u003Ehttps:\/\/www.idahoepscor.org\u003C\/a\u003E\u003C\/p\u003E\n","id":"e696b239-9ecb-412e-b032-03a75b2b9fd6","image_display_url":"https:\/\/dkan.nkn.uidaho.edu\/sites\/default\/files\/Idaho_epscor_logo_no_white_background.png","title":"Idaho EPSCoR","name":"group\/idaho-epscor"},{"description":"\u003Cp\u003EGEM3 is an NSF EPSCoR research program seeking to understand how genetic diversity and phenotypic plasticity affect species response to environmental change, shaping both population response and adaptive capacity.\u003C\/p\u003E\n\u003Cp\u003EVisit them at: \u003Ca href=\u0022https:\/\/www.idahogem3.org\u0022\u003Ehttps:\/\/www.idahogem3.org\u003C\/a\u003E\u003C\/p\u003E\n","id":"1812a312-11a4-492d-960b-9a78b4abfe0c","image_display_url":"https:\/\/dkan.nkn.uidaho.edu\/sites\/default\/files\/GEM3_nov5_logo.png","title":"EPSCoR GEM3","name":"group\/epscor-gem3"}]}]} Error | RCDS Data Repository

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