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2,785 results for “Genotype”
SNP genotyping of indigenous goats of Uganda based on the Goat_IGGC_65K_v2 illumina chip
<p>Uganda's indigenous goats are characterised based on ethnic communities that raise them, average mature weight, and hair coat characteristics. Uganda's indigenous goats have been genotyped based on the Goat_IGGC_65K_v2 illumina chip to study their population structure and genetic characteristics. Information generated from this data is vital for the sustainable utilisation, development, and conservation of Uganda's goat genetic resources.</p>
Data from: Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR
<p>"Mid-density" targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato was developed using the DArTag<sup>TM</sup> technology and later expanded to 4K targets. Genomic markers were selected from the potato Infinium<sup>TM</sup> SNP array to maximize genome coverage and polymorphism rates. The DArTag and SNP array platforms produced equivalent dendrograms in a test set of 298 tetraploid samples, and 83% of the common markers showed good quantitative agreement, with RMSE (root-mean-squared-error) less than 0.5. DArTag is suited for genomic selection candidates in the clonal evaluation trial, coupled with imputation to a higher-density platform for the training population. Using the software polyBreedR, an R package for the manipulation and analysis of polyploid marker data, the RMSE for imputation by linkage analysis was 0.15 in a small half-diallel population (N=85), which was significantly lower than the RMSE of 0.42 with the Random Forest method. Regarding high-value traits, the DArTag markers for resistance to potato virus Y, golden cyst nematode, and potato wart appeared to track their targets successfully, as did multi-allelic markers for maturity and tuber shape. In summary, the potato DArTag assay is a transformative and publicly available technology for potato breeding and genetics.</p>
Diseasome - Finding disease association based on Phenotypic and Genotypic clustering
<p>The final processed phenotypic clustered data (output.zip) from Orphanet is also added along side the genotypic clustering data.</p>
Data from: Analysis of genotyping data reveals the unique genetic diversity represented by the breeds of sheep native to the United Kingdom
<p><strong>Background: </strong>Sheep breeds native to the United Kingdom are noted for high breed variability and exhibit a striking diversity of different traits in phenotypes and genetic diversity. Some of these traits are highly sustainable, such as seasonal wool shedding in the Wiltshire Horn, are likely to become more important as pressures on sheep production increase in coming decades. Despite their clear importance to the future of sheep farming, the genetic diversity of native UK sheep breeds is poorly characterised. This increases the risk of losing the ability to select for breed-specific traits from native breeds that might be important to the UK sheep sector in the future. Here, we use 50K genotyping to perform preliminary analysis of breed relationships and genetic diversity within native UK sheep breeds, as a first step towards a comprehensive characterisation. This study generates novel data for thirteen native UK breeds, including 6 on the UK Breeds at Risk (BAR) list, and utilises existing data from the publicly available Sheep HapMap dataset to investigate population structure, heterozygosity and admixture.</p> <p><strong>Results: </strong>In this study the commercial breeds exhibited high levels of admixture, weaker population structure and had higher heterozygosity compared to the other native breeds, which generally tend to be more distinct, less admixed, and have lower genetic diversity and higher kinship coefficients. Some breeds including the Wiltshire Horn, Lincoln Longwool and Ryeland showed very little admixture at all, indicating a high level of breed integrity but potentially low genetic diversity. Population structure and admixture were strongly influenced by sample size and sample provenance – highlighting the need for equal sample sizes, sufficient numbers of individuals per breed, and sampling across multiple flocks. The genetic profiles both within and between breeds were highly complex for UK sheep, reflecting the complexity in the demographic history of these breeds.</p> <p><strong>Conclusion: </strong>Our results highlight the utility of genotyping data for investigating breed diversity and genetic structure. They also suggest that routine generation of genotyping data would be very useful in informing conservation strategies for rare and declining breeds with small populations sizes. We conclude that generating genetic resources for the sheep breeds that are native to the UK will help preserve the considerable genetic diversity represented by these breeds, and safe guard this diversity as a valuable resource for the UK sheep sector to utilise in the face of future challenges.</p>
Data from: Thermal plasticity in protective wing pigmentation is modulated by genotype and food availability in an insect model of seasonal polyphenism
<p>Phenotypic variation in natural populations results from complex interactions between organisms and their changing environments. The environment shapes both phenotypic frequencies (during adaptation) and organismal phenotypes (through phenotypic plasticity). Developmental plasticity, in particular, refers to the phenomenon whereby an organism's phenotype depends on the environmental conditions during development. It can match phenotype to ecological conditions and help organisms to cope with environmental heterogeneity, including differences between alternating seasons. Experimental studies of developmental plasticity often focus on the impact of individual environmental cues and do not take explicit account of genetic variation. In contrast, natural environments are complex, comprising multiple variables with combined effects that are poorly understood and may vary among genotypes. We investigated the effects of multifactorial environments on the development of the seasonally plastic eyespots of <em>Bicyclus anynana</em> butterflies. Eyespot size depends on developmental temperature and is involved in alternative seasonal strategies for predator avoidance. In nature, both temperature and food availability undergo seasonal fluctuations. However, our understanding of how thermal plasticity in eyespot size varies in response to food availability and across genotypes remains limited. To address this, we investigated the combined effects of temperature (T; two levels: 20°C and 27°C) and food availability (N; two levels: control and limited) during development. We examined their impact on wing and eyespot size in adult males and females from multiple genotypes (G; 28 families). We found evidence of thermal and nutritional plasticity and temperature-by-nutrition interactions (significant TxN) on the size of eyespots in both sexes. Food limitation resulted in relatively smaller eyespots and tempered the effects of temperature. Additionally, we found differences among families for thermal plasticity (significant GxT effects), but not for nutritional plasticity (non-significant GxN effects) nor for the combined effects of temperature and food limitation (non-significant GxTxN effects). Our results reveal the context dependence of thermal plasticity, with the slope of thermal reaction norms varying across genotypes and across nutritional environments. We discuss these results in light of the ecological significance of pigmentation and the value of considering thermal plasticity in studies of the biological impact of climate change.</p>
Supplementary material of "The A1/A2 β-casein genotype of cows, but not their horn status, influences peptide generation during simulated digestion of milk"
<p>Supplementary tables and figures of the research article "The A1/A2 β-casein genotype of cows, but not their horn status, influences peptide generation during simulated digestion of milk"</p>
Phenotypic and genotypic analysis of drug resistance in M. tuberculosis isolates in Gansu, China
<p>Tuberculosis has posed a serious threat to human health. It is imperative to investigate the geographic prevalence of tuberculosis and medication resistance, as this information is essential for informing strategies for its prevention and treatment. Drug resistance was identified using a proportion method. Drug-resistant genes and pathways were predicted using whole genome sequencing. The drug resistance range of bedaquiline was identified using the microporous plate two-fold dilution method, and drug resistance genes were studied using sequencing. The study revealed that 19.99% of the tuberculosis cases had multidrug resistance. The genes of<em> M. tuberculosis</em> are predominantly involved in the synthesis of ABC transporters, two-component systems, and bacterial secretion systems, as well as in energy production and conversion, and lipid transport and metabolism. The genes encode for 82.45% of carbohydrate-related enzymes such as glycoside hydrolases, glycosyl transferases, and carbohydrate esterases. The minimum inhibitory concentration (MIC) of bedaquiline against clinical strains was approximately 0.06 μg/mL, with identified mutations in drug-resistant genes Rv0678, atpE, and pepQ, specifically V152A, P62A, and T222N, respectively. The multidrug resistance tuberculosis development was attributed to the strong medication resistance exhibited. It was concluded that tuberculosis had presented a high level of drug resistance. Phenotypic resistance was related to genes, existing potential genetic resistance in <em>M. tuberculosis</em>. Bedaquiline was found to possess effective antibacterial properties against <em>M. tuberculosis</em>.</p>
Genotypic data from: Lab-based evaluation of the reproductive performance of trojan (MYY) brook trout (Salvelinus fontinalis)
<p>Evaluating the efficacy of the use of trojan male brook trout with two Y chromosomes (M<sub>YY</sub>) requires a better understanding of reproductive performance. We measured the reproductive performance of hatchery age-0 and age-1 M<sub>YY</sub> brook trout compared to hatchery XY males using laboratory crosses. Offspring of XY males had higher survival than offspring of age-1 M<sub>YY</sub> one day post-fertilization but not offspring of age-0 M<sub>YY</sub>. We found no detectable differences in survival from eyed-egg to the juvenile-fry stage. However, size-at-age differed, where offspring of age-0 M<sub>YY</sub> were 3.6% smaller in length and 25.2% smaller in weight than those of XY males. For crosses fertilized by both M<sub>YY</sub> and XY males, we found that a significantly higher proportion of offspring within families were sired by M<sub>YY </sub>versus XY males. These results show, under controlled conditions, evidence for possible fitness advantage for M<sub>YY</sub> under sperm competition, but a possible fitness disadvantage associated with early growth of their offspring. Overall, our results hold promise for the use of M<sub>YY</sub> brook trout to serve as an effective eradication tool. </p>
SNP genotype dataset from brown and anadromous trout
<p>Populations of anadromous brown trout, also known as sea trout, have suffered recent marked declines in abundance due to multiple factors, including climate change and human activities. While much is known about their freshwater phase, less is known about the species' marine feeding migrations. This situation is hindering the effective management and conservation of anadromous trout in the marine environment. Using a panel of 95 single nucleotide polymorphism markers we developed a genetic baseline, which demonstrated strong regional structuring of genetic diversity in trout populations around the English Channel and adjacent waters. Extensive baseline testing showed this structuring allowed the high-confidence assignment of known-origin individuals to the region of origin. This study presents new data on the movements of anadromous trout in the English Channel and southern North Sea. Assignment of anadromous trout sampled from 12 marine and estuarine localities highlighted contrasting results for these areas. The majority of these fisheries are composed predominately of stocks local to the sampling location. However, there were multiple cases of long-distance movements of anadromous trout, with several individuals originating from rivers in northeast England being caught in the English Channel and southern North Sea, in some cases more than 1000 km from their natal region. These results have implications for the management of sea trout in inshore waters around the English Channel and southern North Sea.</p>
Figure 1 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan
Figure 1. Prevalence of four different alleles of Pvmsp-3α (A, B, C and D) from PCR-RFLP
Figure 3 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan
Figure 3. Prevalence of three different alleles of Pvmsp-3β (A, B, C) from PCR-RFLP.
Genotyping measures and population genetic indices for assesing reproductive modes of polyploid Ludwigia grandiflora subsp. hexapetala in western Europe
<p>Raw data used to assess reproductive modes in 53 sampled populations in western Europe (France and northern Spain).</p> <p><em>Ludwigia grandiflora </em>subsp.<em> hexapetala</em> (<em>Lgh</em>) is a hermaphrodite, polyploid, partially clonal and heteromorphic plant that recently colonized multiple countries worldwide. Individuals in this species are either self-incompatible caused by a late-acting self-incompatible (LSI) system developing long-styled flowers, or self-compatible (SC) developing short-styled flowers. We used a SNP approach allowing confident allele dosage to genotype 53 LSI and SC populations of <em>Lgh</em> in France and northern Spain. We measured their genetic diversity and assessed their reproductive modes using methods adapted to autopolyploid species. </p>
Fig. 1 in Evaluating categories of resistance in soybean genotypes from the United States and Brazil to Aphis glycines (Hemiptera: Aphididae)
Fig. 1. Damage level scale (1 to 5); feeding damage caused by Aphis glycines on soybean leaves.
Genotype data of 10 nuclear microsatellite loci for 30 Quercus acutissima populations in China
<p>This dataset includes genotype data of 10 nuclear microsatellite loci for 707 individuals of Quercus acutissima from 30 natural populations in China.</p>
nSSR genotype data for 30 Quercus acutissima populations and 18 Quercus chenii populations in China
<p>This dataset includes genotype data of seven nSSR loci for 696 individuals of Quercus acutissima from 30 natural populations, and 415 individuals of Quercus chenii from 18 natural populations in China.</p>
VCF File containg replicate RAD-seq genotype calls for four Populs alba x Populus tremula hybrids.
<p>VCF file used to estimate RAD-seq genotyping errors in Bresadola et al. (2019).</p>
genotyping matrix for common bean GWAS.
<p>These files inculded twenty phenotypic characteristics were evaluated on 628 accessions. Of these, 15 were quantitative and two were binary traits. Yield-related traits that were evaluated across four locations for three different years.In addition, associations with qualitative traits and 3 datasets for diseases in the greenhouse and insect infestation in a seed chamber were also assessed.</p> <p>In additational, also included genotyping matrix for common bean GWAS.</p>
Changes in Phytochemical Composition and Antioxidant Activity in Nine sh2 Sweet Corn Genotypes during Maturation
<p>Table S1. Mean values ± SD of four biological replicates for the five evaluated traits across nine <em>sh2 </em>sweetcorn hybrids and the five maturity stages. Different lowercase letters as well as different uppercase letters indicate a significant difference at P < 0.05.</p>
Microsatellite genotypes of South African Cape vulture (Gyps coprotheres)
<p>Multilocus microsatellite genotypes of 605 <em>Gyps coprotheres</em> individuals. This first column contains the individual sample identity as provided in Supplementary Data 1 and subsequent columns are allele scores in single row format. Alleles are scored according to their molecular size (in base pairs); missing data is encoded as "0".</p>
Distinguishing mutations and null alleles from genotyping errors using mother progeny comparisons in Brazilian pine (Araucaria angustifolia)
The use of microsatellite markers provides a window into the evolutionary processes of a given species. As such, these markers are widely used in scientific and applied research and are praised for their practicality and ease of use, however, the unavoidable incidence of genotyping deviations has been broadly neglected in the literature. Therefore, the present study aimed to estimate the rate of null alleles, mutations and genotyping errors in microsatellite loci, using Araucaria angustifolia, a threatened species, as a case study. We estimated the rates of the different types of genotyping deviations using mother-progeny genotype comparison from 50 seed-trees and their respective progeny (seeds). A total of 2336 A. angustifolia samples were genotyped, and we found that the rate of null alleles was 0.045. From the 1972 mother-progeny comparisons, the overall genotype deviation rate was 1.58%, consisting of 145 inconsistences (mutations), 339 null alleles and 210 genotyping errors. In terms of seed numbers, 128 (6.5%) showed inconsistencies in at least one locus, 118 (6.0%) null alleles, and 321 (16.3%) genotyping errors. This is the first study to describe the inconsistences (mutations) between mother-progeny genotypes for A. angustifolia, and the outcome makes it clear that an understanding of these genotyping deviations must be considered in assessing the accuracy of inferences made based on population genetics analyses.
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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)
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DANDI Archive for NWB datasets
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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.