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344 results for “genetic testing”
Genetic Relationships Between Terminal Shoot Length, Number of Flushes and Height in a Four-Year-old Progeny Test of Pinus brutia Ten.
<p><strong>Description of the data</strong></p> <p>A total of 188 plus trees were selected from eight natural seed stands of <em>Pinus brutia</em> in the Aegean region of Turkey. The number of trees selected per seed stand (provenance) varied between 7 to 53 trees. Open-pollinated seeds were collected from plus trees in 1998 and in 1999. In addition, six checklots consisting of bulk seeds from natural seed stands were included in the study to estimate genetic gain and link the progeny tests across different breeding zones in the Aegean region.</p> <p>Open-pollinated progeny tests were established at three locations in the Aegean region of Turkey (Hisaronu, Izmir, and Kinik) in March 2000. One-year-old bare-root seedlings were used in the study. Randomized complete block design with four-tree row plots was used in all sites. For each plus tree (female parent), about 72 half-sib progenies were planted across three test sites. The Hisaronu site had four blocks, while two other sites had seven blocks each. Each parent tree was represented by 16 half-sib progenies at the Hisaronu site and 28 progenies in the other two sites when the trials were planted. The spacing among seedlings was 2 x 3 m at each site. Each block was split into four sets (sets in replications) to accommodate a large number of trees, with checklots included in every set. In total, about 166 half-sib progenies and checklots were planted in each block.</p> <p>At the end of the first growing year after planting, survival was assessed. It was about 52% at the Hisaronu site. Dead seedlings at the Hisaronu site were replaced with 1083 two-year-old seedlings of the same families, which were grown in a nursery near Marmaris in the Aegean region. The other two sites had 91% (İzmir) and 94% (Kinik) survival. At age four after planting (2004), tree height (cm), terminal shoot length (cm), and the number of flushes were measured. In total, approximately 12100 trees were assessed across the three locations. </p>
Phlorest phylogeny derived from De Filippo et al. 2012 'Bringing together linguistic and genetic evidence to test the Bantu expansion'
<p>Cite the source of the dataset as:</p> <blockquote> <p>De Filippo, C., Bostoen, K., Stoneking, M., & Pakendorf, B. (2012). Bringing together linguistic and genetic evidence to test the Bantu expansion. Proceedings of the Royal Society B: Biological Sciences, 279(1741), 3256–3263. doi:10.1098/rspb.2012.0318</p> </blockquote>
Summary statistics for association tests between human and Plasmodium falciparum genetic variants in 3,346 severe malaria cases from The Gambia and Kenya
<p>This dataset contains summary statistics for association tests between human and<br> <em>Plasmodium falciparum</em> malaria parasite genetic variants, using data from 3,346 severe malaria cases from The Gambia and Kenya. These results underlie the analysis described in our paper:</p> <p><strong>"Malaria protection due to sickle haemoglobin depends on parasite genotype"</strong></p> <p>Gavin Band, Ellen M. Leffler, Muminatou Jallow, Fatoumatta Sisay-Joof, Carolyne M. Ndila, Alexander W. Macharia, Christina Hubbart, Anna E. Jeffreys, Kate Rowlands, Thuy Nguyen, Sónia M. Gonçalves, Cristina V. Ariani, Jim Stalker, Richard D. Pearson, Roberto Amato, Eleanor Drury, Giorgio Sirugo, Umberto d'Alessandro, Kalifa A. Bojang, Kevin Marsh, Norbert Peshu, Joseph W. Saelens, Mahamadou Diakité, Steve M. Taylor, David J. Conway, Thomas N. Williams, Kirk A. Rockett, Dominic P. Kwiatkowski</p> <p>Nature (2021) doi: <a href="https://doi.org/10.1038/s41586-021-04288-3">10.1038/s41586-021-04288-3</a> <strong>bioRxiv link</strong>:: <a href="https://doi.org/10.1101/2021.03.30.437659">doi.org/10.1101/2021.03.30.437659</a><br> <br> The genotype data underlying these summary statistics has also been deposited on Zenodo<br> (<a href="https://zenodo.org/record/4973477">doi:10.5281/zenodo.4973477</a>). The <a href="https://www.well.ox.ac.uk/~gav/hptest)">HPTEST software</a> used to generate these results has also been deposited (<a href="https://doi.org/10.5281/zenodo.5685580">doi:10.5281/zenodo.5685580</a>). Please see the <a href="https://www.malariagen.net/resource/32">MalariaGEN website</a> for a full list of datasets which have been released with this manuscript.</p> <p><strong>Data contents.</strong></p> <p>The dataset consists of a single <a href="http://sqlite.org">sqlite database file</a> containing the results, and an accompanying README file in markdown and html format. Please see the README file for full details of the data contents.</p> <p> </p>
A genome-wide test for paternal indirect genetic effects on lifespan in Drosophila melanogaster
<p>Exposing sires to various environmental manipulations has demonstrated that paternal effects can be non-trivial also in species where male investment in offspring is almost exclusively limited to sperm. Whether paternal effects also have a genetic component (i.e. paternal indirect genetic effects - PIGEs) in such species is however largely unknown, primarily because of methodological difficulties separating indirect from direct effects of genes. PIGEs may nevertheless be important, since they have the capacity to contribute to evolutionary change. Here we use Drosophila genetics to construct a breeding design that allows testing nearly complete haploid genomes (>99%) for PIGEs. Using this technique, we estimate the variance in male lifespan due to PIGEs among four populations and compare this to the total paternal genetic variance (the sum of paternal indirect and direct genetic effects). Our results indicate that a substantial part of the total paternal genetic variance results from PIGEs. A screen of 38 haploid genomes, randomly sampled from a single population, suggests that PIGEs also influence variation in lifespan within populations. Collectively, our results demonstrate that PIGEs may constitute an underappreciated source of phenotypic variation.</p>
"Do you want to know who you are?" The rise of genetic ancestry testing and the search for genealogies: an anonymized survey from Sweden
<p>Full, anonymized survey data on genetic genealogy, ancestry and identity conducted by the Swedish Genealogical Society as part of a research project funded by the HERA joint research program "Uses of the Past"</p>
Fig. 2 in Testing microsatellite loci and preliminary genetic study for Eurasian otter in South Korea
Fig. 2. Locations of sampling for tissue (1. Hoengseong-gun, Gangwon-do, 2. Uljin-gun, Gyeongsangbuk-do, 3. Jeongeup-si, Jeollabukdo, 4. Muju-gun, Jeollabuk-do, 5. Hampyeong-gun, Jeollanam-do).
BRAIN Journal-High Performance Data mining by Genetic Neural Network-Figure 7 . Test Accuracy with prograess generation
<p>In the training phase, the neural network weights errors are minimized and network design<br> problem which the objective function to an acceptable level. In test step we have better results<br> because weights of neural network are adjusted by genetic algorithm and back propagation method.<br> Of course achievement to accuracy with 83.5% is reason using of good feature with minimum error.</p>
Data on Direct-to-Consumer Genetic Testing and DNA testing companies
<p>This table was compiled between 2011 and 2018. It is a list of companies offering direct-to-consumer DNA tests over the internet. It is primarily concerned with direct-to-consumer genetic testing companies operating currently and also includes those, which are no longer operating. The table briefly summarizes the services offered by each company and gives the company’s location.</p> <p>I am continuing to update this list, so it is a work in progress, it does include some companies that advertise their services to physicians and some companies may have altered their offerings. Further updates will be provided later in 2018. I have added a shorter table at the end of relevant other companies. I hope to make a searchable database of a revised version of the document available through my website in the future.</p> <p>This work is being released for informational and educational purposes and should not be used for commercial purposes.</p> <p>Please refer to my website for further updates <a href="http://www.andelkamphillips.com">http://www.andelkamphillips.com</a></p>
Testing the effectiveness of genetic monitoring using genetic non-invasive sampling
<p>1. Effective conservation requires accurate data on population genetic diversity, inbreeding, and genetic structure. Increasingly, scientists are adopting genetic non-invasive sampling as a cost-effective population-wide genetic monitoring approach. Genetic non-invasive sampling has, however, known limitations which may impact the accuracy of downstream genetic analyses.</p> <p>2. Here, using high quality SNP data from blood/tissue sampling of a free-ranging koala population (n = 430), we investigated how the reduced SNP panel size and call rate typical of genetic non-invasive samples (derived from experimental and field trials) impacts the accuracy of genetic measures, and also the effect of sampling intensity on these measures.</p> <p>3. We found that genetic non-invasive sampling at small sample sizes (14% of population) can provide accurate population diversity measures, but slightly underestimated population inbreeding coefficients. Accurate measures of internal relatedness required at least 33% of the population to be sampled. Accurate geographic and genetic spatial autocorrelation analysis requires between 28% and 51% of the population to be sampled.</p> <p>4. We show that genetic non-invasive sampling at low sample sizes can provide a powerful tool to aid conservation decision-making and provide recommendations for researchers looking to apply these techniques to free-ranging systems.</p>
Reference datasets for consistency tests of GENAPOPOP 1.0 software: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms.
<p>Datasets companion of the manuscript entitled GenAPoPop 1.0: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms, used to achieve consistency test with Spagedi 1.5 software, and used as reference datasets to demonstrate the new possibilities allowed by GenAPoPop software.</p> <p>Raw datasets used for testing GenAPoPop 1.0, A user-friendly software for easily compute genetic analyses of autopolyploid populations packaged for Linux, MacOS and Windows; Results obtained from Spagedi 1.5 (Hardy & Vekemans 2001) and GenAPoPop1.0.</p> <p>Four pseudo-observed genotyping autotetrapolyploid SNP datasets, corresponding respectively to panmictic (A), highly clonal (B), highly selfed (C) and half-clonal-half-selfed (D) reproductive mode scenario. In all these four scenarios, we simulated two populations of 100 individuals each, connected with a migration rate of 0.01 and mutating at a rate of 0.01, genotyped at 10 SNPs. Datasets were recorded 1000 generations after an initial randomly drawing population with equal allele frequencies.</p> <p>One SNP tetraploid genotyping dataset from two French <em>Ludwigia grandiflora subsp. hexapetala</em> populations (aquatic plant from the Angiosperm clade): two populations in which we collected 75 individuals, each genotyped with 36 SNPs using the Hiplex method allowing confident allele dosage (Delord et al. 2018).</p> <p>One microsatellite tetraploid genotyping dataset on two Aulactinia stella populations (sea-anemone from the Cnidaria phylum), sampled on the coast of the arctic ocean. One population of 21 individuals and one population of 15 individuals, both genotyped with 10 microsatellites.</p> <p>We also report here the consistency tests with GenAlex and Spagedi, results of analyses (GPP tab) on 6300 independant simulations and inferences of the quantitative reproductive modes using the bayesian method on CEMP tab made on 6300 another independant simulations.</p>
figure 6 Mantel test for A in Spatial genetic structure in the Eurasian otter (Lutra lutra) meta-population from its core range in Italy
figure 6 Mantel test for A) the correlation between geographic distance (GGDsq) and genetic distance (LinGD) (Rxy = 0.264, P = 0.0001) and for B) the correlation between resistance distance (a measure of ecological distance) (ECO500) and LinGD (Rxy = 0.217, P = 0.0001).
Testing the effectiveness of genetic monitoring using genetic non-invasive sampling
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Data from: Testing the evolutionary potential of an alpine plant: Phenotypic plasticity in response to growth temperature outweighs parental environmental effects and other genetic causes of variation
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Genetic testing predicts appearance but not behavior in dogs
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A genome-wide test for paternal indirect genetic effects on lifespan in Drosophila melanogaster
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Strong genetic structure in a widespread estuarine crab: A test of potential versus realized dispersal
<p>Aim: Genetic structure has proven difficult to predict for marine and estuarine species with multi-day pelagic larval durations, since many disperse far less than expected based on passive transport models. In such cases, the gap between potential and realized dispersal may result from larval behaviors that evolved to facilitate retention and settlement in favorable environments. Behavior is predicted to play a particularly key role in structuring truly estuarine species, which often moderate their behavior to remain within their natal estuaries. In such systems, this restricted dispersal may lead to high divergence, local adaptation, and eventual speciation across their range. Here, we test whether a geographically widespread estuarine crab, known to have behavior promoting larval retention, exhibits high population structure despite a 2-4 week larval duration.</p> <p>Location: Atlantic and Gulf Coasts of North America Taxon: White-fingered mud crab, Rhithropanopeus harrisii</p> <p>Methods: Population genomic analyses across nine estuaries from New Hampshire to Louisiana using 12,638 transcriptome-derived SNPs.</p> <p>Results: We found highly differentiated genetic signatures among all nine estuaries, separated by 200-5,000 km of coastline. Estimates of gene flow suggest that migration is low and largely symmetrical between sites. We also observed deep phylogenetic divides corresponding to major biogeographic breaks.</p> <p>Main conclusions: These results indicate substantial and longstanding constraints to dispersal in the species' native range, likely arising from the emergence of geological and oceanographic barriers and sustained by behavior that promotes estuarine retention during larval development. This work supports the idea that larval behavior promoting estuarine retention can be reflected in substantial genetic structure even in species with multi-week pelagic larval durations. Such behavior-restricted dispersal has implications for predicting adaptation and spread in estuarine species, many of which have been introduced outside their native ranges.</p>
Data and Code: No support for the genetic hypothesis of the Black-white achievement gap using polygenic scores and tests for divergent selection
<p>Data and Code for article "No support for the genetic hypothesis of the Black-white achievement gap using polygenic scores and tests for divergent selection"</p>
Identifying diagnostic genetic markers for a cryptic invasive agricultural pest: a test case using the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae)
Insect pests destroy ~15% of all USA crops, resulting in losses of $15 billion annually. Thus, developing cheap, quick and reliable methods for detecting harmful species is critical to curtail insect damage and lessen economic impact. The apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae), is a major invasive pest threatening the multibillion-dollar apple industry in the Pacific Northwest USA. The fly is also sympatric with a benign but morphologically similar and genetically closely related species, R. zephyria, which attacks non-commercial snowberry. Unambiguous species identification is essential due to a zero-infestation policy of apple maggot for fruit export. Mistaking R. zephyria for R. pomonella triggers unnecessary and costly quarantines, diverting valuable control resources. Here we develop and apply a relatively simple and cost-effective diagnostic approach using Illumina sequencing of double digest restriction-site associated DNA markers. We identified five informative single nucleotide polymorphisms (SNPs) and designed a diagnostic test based on agarose gel electrophoresis of restriction enzyme digested polymerase chain reaction amplification products (RFLPs) to distinguish fly species. We demonstrated the utility of this approach for immediate, one day species identification by scoring apple- and snowberry-infesting flies of known host plant identity, reared directly from 11 sites throughout Washington. However, if immediate diagnosis is not required, or hundreds to thousands of specimens must be assessed, then a direct Illumina-based sequencing strategy, similar to that used here for diagnostic SNP identification can be powerful and cost-effective. The genomic strategy we present is effective for R. pomonella and also transferable to many cryptic pests.
Data from: The molecular biogeography of the Indo-Pacific: testing hypotheses with multispecies genetic patterns
Aim: To test hypothesized biogeographic partitions of the tropical Indo-Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test. Location: The Indo-Pacific Ocean. Time Period: Pliocene through the Holocene. Major Taxa Studied: 56 marine species. Methods: We tested eight biogeographic hypotheses for partitioning of the Indo-Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis were evaluated for pairwise ΦST, and these ΦST distributions were compared to distributions from randomized datasets and simple coalescent simulations of vicariance arising from the Last Glacial Maximum. We then weighed the relative contribution of distance vs. environmental or geographical barriers to pairwise ΦST with a distance-based redundancy analysis (dbRDA). Results: We observed a diversity of outcomes, although the majority of species fit a few broad biogeographic regions. Repeated coalescent simulation of a simple vicariance model yielded a wide distribution of pairwise ΦST that was very similar to empirical distributions observed across five putative barriers to gene flow. Three of these barriers had median ΦST that were significantly larger than random expectation. Only 21 of 52 species analyzed with dbRDA rejected the null model. Among these, 15 had overwater distance as a significant predictor of pairwise ΦST, while 11 were significant for geographical or environmental barriers other than distance. Main Conclusions: Although there is support for three previously described barriers, phylogeographic discordance in the Indo-Pacific oceans indicates incongruity between processes shaping the distributions of diversity at the species and population levels. Among the many possible causes of this incongruity, genetic drift provides the most compelling explanation: given massive effective population sizes of Indo-Pacific species, even hard vicariance for tens of thousands of years can yield ΦST values that range from 0 to nearly 0.5.
Fig.1 in Testing The Microsatellites-Pcr Markers For Genetic Diversity Research Of Alien Ponto-Caspian Amphipod Pontogammarus Robustoides G. O. Sars, 1894
Fig.1. Localities of sampling sities in the Latvian reservoirs.
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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.
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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.