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1,019 results for “SNP”
Fig. 2 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum
Fig. 2 (a) Measurement of capsule orientation in relation to the seta in Homalothecium as the angle (in degrees) between the seta and spore capsule at the basis of the spore capsule. (b) Capsule inclinations of individuals from the allopatric populations fell into the black ranges of variation; in the sympatric populations individuals occurred with capsule inclinations ranging outside typical capsule inclinations of the pure species (red zone: 150°- 164°), indicating hybrid origin
SNP genotypes for 524 wild mice and selected laboratory strains
<p>SNP genotypes from the Mouse Universal Genotyping Array for 524 wild mice and 12 selected laboratory strains. Data are provided in PLINK binary format (*.bed/*.bim/*.fam files) with an accompanying sample manifest (comma-separated text.)</p>
SNP call data for: The current epidemic of the barley pathogen Ramularia collo-cygni derives from a recent population expansion and shows global admixture
<p>Ramularia Leaf Spot is becoming an ever increasing problem in main barley growing regions since the 1980s, causing up to 70% yield loss in extreme cases. Yet, the causal agent <em>Ramularia collo-cygni</em>, remains poorly studied. The diversity of the pathogen in the field thus far remains unknown. Furthermore, it is unknown to which extend the pathogen has a sexual reproductive cycle. To date, the teleomorph of <em>R. collo-cygni</em> has not been observed.</p> <p>To study the genetic diversity of <em>R. collo-cygni </em>and to get more insights into its biology, we sequenced the genomes of 19 <em>R. collo-cygn</em>i isolates from multiple geographic locations and diverse hosts. Here we share the SNP call data as well as the reference genome.</p> <p>The reference genome files and assembly can be found on ENI: GCA_900074925.1</p> <p>https://www.ebi.ac.uk/ena/data/view/GCA_900074925.1</p> <p>The raw sequence data is also available through ENI: ERX2296228</p> <p>https://www.ebi.ac.uk/ena/data/view/ERX2296228</p>
Baboon and Gelada SNP Calls VCF
<p>Bgzipped vcf and tabix index files of baboon and gelada SNP calls of 16 individuals on the papAnu2 assembly as published in Rogers et al. (2019). The comparative genomics and complex population history of Papio baboons. Science Advances. 30 Jan 2019: Vol. 5, no. 1, eaau6947 DOI: 10.1126/sciadv.aau6947.</p>
SNP data for the SwAsp collection
<p>DNP data for 94 individuals from the SwAsp collection, described in Luquez et al. (2008). Details about sequencing and SNP calling can be found in Wang et al. (2018). Data is mapped agains the <em>P. tremula </em>genome assembly v1.1(Lin et al. 2018).</p> <p><strong>References</strong></p> <p><strong><strong><strong>Lin Y-C</strong>, <strong>Wang J</strong>, <strong>Delhomme N</strong>, <strong>Schiffthaler B</strong>, <strong>Sundström G</strong>, <strong>Zuccolo A</strong>, <strong>Nystedt B</strong>, <strong>Hvidsten TR</strong>, <strong>de la Torre A</strong>, <strong>Cossu RM</strong>, <em>et al.</em></strong></strong> <strong>2018</strong>. Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. <em>Proceedings of the National Academy of Sciences of the United States of America</em> <strong>115</strong>: E10970–E10978.</p> <p><strong><strong>Luquez V</strong>, <strong>Hall D</strong>, <strong>Albrectsen BR</strong>, <strong>Karlsson J</strong>, <strong>Ingvarsson P</strong>, <strong>Jansson S</strong></strong>. <strong>2008</strong>. Natural phenological variation in aspen (<em>Populus tremula</em>): the SwAsp collection. <em>Tree Genetics & Genomes</em> <strong>4</strong>: 279–292.</p> <p><strong><strong><strong>Wang J</strong>, <strong>Ding J</strong>, <strong>Tan B</strong>, <strong>Robinson KM</strong>, <strong>Michelson IH</strong>, <strong>Johansson A</strong>, <strong>Nystedt B</strong>, <strong>Scofield DG</strong>, <strong>Nilsson O</strong>, <strong>Jansson S</strong>, <em>et al.</em></strong></strong> <strong>2018</strong>. A major locus controls local adaptation and adaptive life history variation in a perennial plant. <em>Genome Biology</em> <strong>19</strong>: 72.</p>
SNP Data for Aedes aegypti populations in Florida and southern California
<p>In the affiliated paper we compare likely the oldest populations of <i>Aedes aegypti</i> in continental North America with some of the newest to illuminate the range of genetic diversity and structure that can be found within the invasive range of this important disease vector. <i>Aedes aegypti</i> populations in Florida have likely persisted since the 1600-1700s, while populations in southern California derive from new invasions that occurred in the last ten years. For this comparison, we genotyped 1,193 individuals from 29 sites at 12 highly variable microsatellites and a subset of these individuals at 23,961 single nucleotide polymorphisms (SNPs). This dataset contains the SNP genetic information.</p>
Genome-wide SNP discovery in native American and Hungarian Robinia pseudoacacia genotypes using next-generation double-digest restriction-site-associated DNA sequencing (ddRAD-Seq)
<p>Initial filtered ddRADseq dataset with highly variable SNP markers from native American and Hungarian <em>Robinia pseudoacacia</em> L. individuals</p>
A combination of HLA-DP α and β chain polymorphisms paired with a SNP in the DPB1 3' UTR region, denoting expression levels, are associated with Atopic Dermatitis
<p>The publication "A combination of HLA-DP α and β chain polymorphisms paired with a SNP in the DPB1 3’ UTR region, denoting expression levels, are associated with Atopic Dermatitis" contains analysis from two different cohorts: Genetics in Atopic Dermatitis (GAD), which is the main dataset, and Pediatric Eczema Elective Registry (PEER), which is the replication cohort. Included herein are the HLA Class II genotypes for both the GAD and PEER cohorts at 2-field resolution, which forms the basis for the analysis included in the publication. (DOI: 10.3389/fgene.2023.1004138)</p>
Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data
<p>Knowledge on the genetic composition of <em>Quercus petraea</em> in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-tag sequences to the <em>Quercus robur</em> reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of <em>Q. petraea</em> were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north–southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4–16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined <em>Q. petraea</em> populations.</p>
SNP weightings used for a PRS of melanoma risk
<p>The weightings for genetic markers utilized in PRS generation, were derived from independant SNP effect estimate significant at P value < 5e-7) from an adapted iteration of the most recent GWAS meta-analysis on melanoma risk from Landi et al. (Nat Gen, 2020. https://doi.org/10.1038/s41588-020-0611-8). This modified version excluded data from the Brisbane Nevus Morphology Study and the QSkin cohorts, but substantial cohorts such as 23andMe, Inc and UK Biobank were retained.</p> <p>provided are: chromosome, base position (build 37), A1 (effect allele), A2 (non effect allele), P value and odds ratio (OR)</p>
SNP Data for Aedes aegypti populations in Florida and southern California
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70K SNP array data for Lumpfish (Cyclopterus lumpus) across the trans-Atlantic
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Planform change and Fundulus SNP data for small watersheds in South Mississippi and Louisiana
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Anolis carolinensis character displacement SNP
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Annotated genes harboring major effect markers (R2 ≥ 15%). Highlighted in green are genes annotated from Rhodes et al. 2014,2017, in orange genes annotated as similar to Peroxidase, in yellow new annotations from sorghum genome in Atlas. In the first three columns start and stop position on the sorghum genome and transcript name, followed by the nearest marker name and the distance of the gene from the nearest marker, then a column where are shown the GWAS methods and target traits for which the linked SNP was significant, the last column shows the category of the genes.
<p><strong>We conducted a comprehensive genomics study to map genomic loci determining the production of antioxidants in sorghum grains. Encouraging results were obtained and published in peer-reviewed article with impact factor (https://doi.org/10.1371/journal.pone.0225979). Annotated genes harboring major effect markers (R<sup>2</sup> ≥ 15%) were identified and will be of worldwide interest. </strong></p>
Data from: Candidate gene SNP variation in floodplain populations of pedunculate oak (Quercus robur L.) near the species' southern range margin: weak differentiation yet distinct associations with water availability
<p>Populations residing near species' low-latitude range margins (LLM) often occur in warmer and drier environments than those in the core range. Thus, their genetic composition could be shaped by climatic drivers that differ from those occurring at higher latitudes, resulting in potentially adaptive variants of conservation value. Such variants could facilitate the adaptation of populations from other portions of the geographic range to similar future conditions anticipated under ongoing climate change. However, very few studies have assessed standing genetic variation at potentially adaptive loci in natural LLM populations. We investigated standing genetic variation at SNPs located within 117 candidate genes and its links to putative climatic selection pressures across 19 pedunculate oak (Quercus robur L.) populations distributed along a regional climatic gradient near the species' southern range margin in southeastern Europe. These populations are restricted to floodplain forests along large lowland rivers, whose hydric regime is undergoing significant shifts under modern rapid climate change. The populations showed very weak geographic structure, suggesting extensive genetic connectivity and gene flow or shared ancestry. We identified eight (6.2%) positive FST-outlier loci, and genotype-environment association analyses revealed consistent associations between SNP allele frequencies and several climatic variables linked to water availability. A total of 61 associations involving 37 SNPs (28.5%) from 35 annotated genes provided important insights into putative functional mechanisms in our system. Our findings provide empirical support for the role of LLM populations as sources of potentially adaptive variation that could enhance species' resilience to climate change-related pressures.</p>
Rhesus Macaque SNP Calls VCFs
<p>Bgzipped vcf and tabix index files of rhesus macaque SNP calls of 150 individuals on the rheMac8 assembly. The samples are all males from the Tulane National Primate Research Center.</p>
SNP datasets obtained with ddRADseq from four contact zones between Podarcis carbonelli and four other Podarcis species
<p><span><span><span>We used double digestion restriction site associated DNA (ddRAD) sequencing to discover SNPs in samples from four contact zones between <i>Podarcis carbonelli</i> and four other <em>Podarcis</em> species</span></span>. We obtained a panel of SNPs for each for each contact zone and reference populations and a dataset of diagnostic SNPs between reference populations for each contact zone but excluding private alleles from references, i.e. excluding alleles that are not present in the populations of contact. The final datasets (complete and diagnostic) were obtained after removing loci with depth coverage <8, missing data >20% and removing individuals with more than 35% of missing data. Across complete and diagnostic datasets, mean coverage by individuals ranged from 28 to 47 and by loci from 28 to 44<span><span>. The analysis of replicate samples (about 6% of samples were replicated, i.e. were amplified and sequenced in independent libraries and SNP calling was performed independently) showed high levels (>99%) of multilocus genotype replicability.</span></span></span></p>
Color scores, COI haplotypes and SNP data for Phelotrupes auratus individuals
<p>We studied the population genetic structure underlying the geographic variation in the structural color of the geotrupid dung beetle, <i>Phelotrupes auratus</i>,<i> </i>which exhibits metallic body colors of different reflectance wavelengths perceived as red, green, and indigo. These forms occur parapatrically in an area of Japan. The color variation was not related to variation in climatic factors. Using single-nucleotide polymorphisms (SNPs) from restriction-site associated DNA sequences, we discriminated five groups of populations (west/red, south/green, south/indigo, south/red, and east/red) by a combination of genetic clusters (west, south, and east) and three color forms. There were three transition zones for the color forms: two between the red and green forms were hybrid zones with steep genetic clines, which implies the existence of barriers to gene flow between regions with different colors. The remaining transition zone between the green and indigo forms lacked genetic differentiation, despite the evident color changes, which implies regionally specific selection on the different colors. In a genome-wide association study, we identified four SNPs that were associated with the red/green or indigo color and were not linked with one another, which implies that the coloration was controlled by multiple loci, each affecting the expression of a different color range. These loci may have controlled the transitions between different combinations of colors. Our study demonstrates that geographic color variation within a species can be maintained by nonuniform interactions among barriers to gene flow, locally specific selection on different colors, and the effects of different color loci.</p>
Feline 60K SNP chip data originated from the domestic cat in Japan
<p>Pedigreed cats have traditionally been mated with close relatives, which increases the risks for inbreeding depression and genetic disorders. We evaluated the genome-wide population structure and the degree of inbreeding of 1022 cats, including 13 pedigreed and two random bred populations from Japan and the USA, using single nucleotide polymorphism array-based data. </p>
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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.