Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
16
datasets available to search
ShareScore release 0.7.1
Dataset results
16 results for “SNP panel”
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
<p>DNA 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. </p> <p><em>DNA Extraction:</em> Extraction of DNA from caudal fin tissues were performed using Quick-DNA Miniprep Plus purification kits (Zymo Research Inc.©). Small sections of fin tissue (≤ 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.©) and proteinase K. All tissues were digested in sealed microcentrifuge tubes for at minimum 3 h at 55°C in a water bath. We then aliquoted 100 µL of digestion supernatant and combined with 200 µL of genomic binding buffer (Zymo Research Inc.©). DNA was eluted in 50, 75, and 100 µL 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 µL of elution buffer used.</p> <p><em>Genotyping:</em> Following extraction, genotyping-in-thousands sequencing took place at the Hagerman National Fish Hatchery’s 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.</p> <p><strong>Ancillary peer-reviewed manuscripts:</strong><br> <em>Genotyping protocols</em><br> 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. https://doi.org/10.1111/1755-0998.12357<br> <em>SNP loci reference</em><br> Collins 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. https://doi.org/10.1002/ece3.6641 </p> <p><strong>Data Use</strong>:<br> <em>License</em>: <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> <br> <em>Recommended Citation</em>: 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. https://doi.org/10.5281/zenodo.7055582</p> <p>Funding for this project is provided by US National Science Foundation and Idaho EPSCoR through award: OIA-1757324 </p>
Pakistani historical wheat panel 37K SNP data
<p>A collection of 196 historical wheat cultivars of Pakistan released between 1911 to 2022 were subjected to DNA fingerprinting using 16K genotyping-by-targeted sequencing (GBTS) platform. This platform is based on NGS and the 16K probes were resequenced. The resequencing data was aligned to Chinese Spring RefSeq version 1.1 and SNPcalling was performed. This resulted in 37K mSNP (multiple SNPs) DNA fingerprinting data. This is thus far the most comprehensive DNA fingerprinting data of all released cultivars of wheat so far. This data is publically available and can be used in research and publications subject to the acknowledgement. </p>
Development of a SNP panel for geographic assignment and population monitoring of jaguars (Panthera onca)
Open the record for dataset details and reuse information.
Genomic prediction for growth using a low-density SNP panel in dromedary camels
Open the record for dataset details and reuse information.
Development of a panel of SNP loci in the emblematic southern damselfly (Coenagrion mercuriale) using a hybrid method: Pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species
Open the record for dataset details and reuse information.
Pakistani historical wheat panel 37K SNP data
Open the record for dataset details and reuse information.
Development of a cost-effective, multifunctional SNP panel and analysis workflow for wolf monitoring in Finland
Open the record for dataset details and reuse information.
Data from: Use of genotyping-by-sequencing data to develop a high-throughput and multi-functional SNP panel for conservation applications in Pacific lamprey
Open the record for dataset details and reuse information.
Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes
<p>Cichlid fish of the genus <i>Oreochromis</i> form the basis of the global tilapia aquaculture and fisheries industries. Broodstocks for aquaculture are often collected from wild populations, which in Africa may be from locations containing multiple <i>Oreochromis </i>species. However, many species are difficult to distinguish morphologically, hampering efforts to maintain good quality farmed strains. Additionally, non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native <i>Oreochromis </i>species, which themselves are important for capture fisheries. The morphological identification of these hybrids is particularly unreliable. Here, we describe the development of a single nucleotide polymorphism (SNP) genotyping panel from whole-genome resequencing data that enables targeted species identification in Tanzania. We demonstrate that an optimized panel of 96 genome-wide SNPs based on F<sub>ST</sub> outliers performs comparably to whole genome resequencing in distinguishing species and identifying hybrids. We also show this panel outperforms microsatellite-based and phenotype-based classification methods. Case studies indicate several locations where introduced aquaculture species have become established in the wild, threatening native <i>Oreochromis</i> species. The novel SNP markers identified here represent an important resource for assessing broodstock purity in hatcheries and helping to conserve unique endemic biodiversity.</p>
Data from: Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples
Open the record for dataset details and reuse information.
Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes
Open the record for dataset details and reuse information.
Genome-wide SNP array data from Human Variation Panel by Illumina 550K
GEO Series GSE24260. Homo sapiens. 192 samples. Type: SNP genotyping by SNP array; Genome variation profiling by SNP array.
Genome-wide SNP array data from Human Variation Panel by Illumina 650K
GEO Series GSE24274. Homo sapiens. 95 samples. Type: SNP genotyping by SNP array; Genome variation profiling by SNP array.
Genome-wide SNP array data from Human Variation Panel by Illumina 510S
GEO Series GSE24245. Homo sapiens. 288 samples. Type: SNP genotyping by SNP array; Genome variation profiling by SNP array.
Single Nucleotide Polymorphism (SNP) Panels and Risk Assessment in Women Undergoing Mammography
ClinicalTrials.gov study NCT01124019. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A comprehensive assessment of a newly designed non-exonic SNP-based NGS panel for HRD detection
GEO Series GSE203509. Homo sapiens. 27 samples. Type: Genome variation profiling by SNP array.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.