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2,785 results for “genotyping”
A specific IL6 polymorphic genotype modulates the risk of T. cruzi parasitemia while IL18, IL17A and IL1B variant profiles and HIV infection protect against cardiomyopathy in Chagas disease
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Genotype data for: Demographic and genetic consequences of a steelhead supplementation program
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Patterns of genotype-environment association in the eastern North American yellow birch (<em>Betula alleghaniensis</em> Britt.)
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Genotypic data from: Lab-based evaluation of the reproductive performance of trojan (MYY) brook trout (Salvelinus fontinalis)
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Microsatellite genotypes of A. chlorotica parentage analysis
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Data from: Analysis of genotyping data reveals the unique genetic diversity represented by the breeds of sheep native to the United Kingdom
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Data for: Russian honey bee genotype identification through enhanced marker panel set
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Data from: Plasticity in hydraulic architecture: Riparian trees respond to increased temperatures with genotype-specific adjustments to leaf traits
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Genotype-environment interactions shape leaf functional traits of cacao in agroforests
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Genotyping-by-sequencing of Canada’s Apple Biodiversity Collection
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An experimental test of parasite adaptation to common vs. rare host genotypes
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Cytotype and genotype predict mortality and recruitment in Colorado quaking aspen (Populus tremuloides)
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SNP genotypes of the international institute of tropical agriculture Cowpea Core
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Data from: A socially polymorphic Formica ant species exhibits a novel distribution of social supergene genotypes
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Genotypes for GWAS study on feed efficiency traits in rabbits
<p>Dataset with genotypes on rabbits</p>
Incremental integration for tracking genotype-phenotype associations - dataset snapshot
<p>This dataset is an archive of data and code files used to generate figures and tables for a manuscript entitled "Incremental integration for tracking genotype-phenotype associations".</p> <p>Data files include the exact versions of raw materials as well as databases produced during the course of the analysis described in the manuscript. </p> <p>Code files include python and R components.</p> <p>Further details are available in the archive README file.</p>
CCLid: A toolkit to authenticate the genotype and stability of cancer cell lines
<p>CCLid (Cancer Cell Line identification) is designed as a toolkit to address the lack of a publicly available resource for genotype-based cell line authentication. We developed this resource to allow for genotype-matching of any given cancer cell line to the 1,204 unique cell lines found in the CCLE dataset, with support to include additional SNP array datasets. Using the B-allele frequencies (BAFs) for all SNPs found in common between the input data and reference datasets, this tool will allow for a genotype matching operation that trains and uses a logistic model to calculate the probability of the best cell line matches. This is followed by a measure of genetic drift between isogenic lines by look for segments of the genome that have significantly different BAF values.</p> <p> </p> <p>This zenodo dataset contains the (sample x probeset) BAF matrix for the CCLE dataset, as well as supporting datasets to allow mapping of SNP probesets and genotype correction between SNP array technologies (i.e. Affymetrix SNP 6.0 and Illumina HumanOmni 2.5M). This also contains all the metadata for cell line identities in CCLE, GDSC, and gCSI as well their corresponding cellosaurus unique identifies.</p>
Microsatellite genotypes of Pomatoschistus microps and Pomatoschistus marmoratus of southern France lagoons
<p><i>Pomatoschistus marmoratus </i>and <i>Pomatoschistus microps</i> are small sedentary gobies inhabiting the lagoons of European Mediterranean and Atlantic coasts. Along the French Mediterranean coast their respective geographical distribution is not precisely known, in part because they are cryptic species. In this study, 512 gobies of both species were caught as 17 samples in 12 lagoons of the <i>Golfe du Lion</i> on the French Mediterranean coast. They were genotyped at six microsatellite loci and investigated statistically using multidimensional analyses, Bayesian assignment (<span>Structure</span>) and <span>Newhybrids</span> classification. This allowed us to describe the contrasted distribution of each species (<i>P. microps</i> in the east, <i>P. marmoratus</i> in the west), with several exceptions. Neither geographic structure nor isolation by distance was detected among differentiated populations of each species. The suggested mechanism is a deep sedentary behaviour associated with foundations following extinctions. The two species are sympatric or even in syntopy in 5 or 6 sampled lagoons producing rare fertile hybrids.</p>
Data from: Genotyping-in-Thousands by sequencing reveals marked population structure in Western Rattlesnakes to inform conservation status
<p>Delineation of units below the species level is critical for prioritizing conservation actions for species at-risk. Genetic studies play an important role in characterizing patterns of population connectivity and diversity to inform the designation of conservation units, especially for populations that are geographically isolated. The northernmost range margin of Western Rattlesnakes (<em>Crotalus oreganus</em>) occurs in British Columbia, Canada, where it is federally classified as threatened and restricted to five geographic regions. In these areas, Western Rattlesnakes hibernate (den) communally, raising questions about connectivity within and between den complexes. At present, Western Rattlesnake conservation efforts are hindered by a complete lack of information on genetic structure and degree of isolation at multiple scales, from the den to the regional level. To fill this knowledge gap, we used Genotyping-in-Thousands by sequencing (GT-seq) to genotype an optimized panel of 362 single nucleotide polymorphisms (SNPs) from individual samples (n = 461) collected across the snake's distribution in western Canada and neighboring Washington (USA). Hierarchical STRUCTURE analyses found evidence for population structure within and among the five geographic regions in BC, as well as in Washington. Within these regions, 11 genetically distinct complexes of dens were identified, with some regions having multiple complexes. No significant pattern of isolation-by-distance and generally low levels of migration were detected among den complexes across regions. Additionally, snakes within dens generally were more related than those among den complexes within a region, indicating limited movement. Overall, our results suggest that the single, recognized designatable unit for Western Rattlesnakes in Canada should be re-assessed to proactively focus conservation efforts on preserving total genetic variation detected range wide. More broadly, our study demonstrates a novel application of GT-seq for investigating patterns of diversity in wild populations at multiple scales to better inform conservation management.</p>
Inland walleye genotypes
<p>Targeted amplicon sequencing methods, such as genotyping-in-thousands by sequencing (GT-seq), facilitate rapid, accurate, and cost-effective analysis of hundreds of genetic loci in thousands of individuals. Development of GT-seq panels is non-trivial, but studies describing trade-offs associated with different steps of GT-seq panel development are rare. Here, we construct a dual-purpose GT-seq panel for walleye (<i>Sander vitreus</i>), discuss trade-offs associated with different development and genotyping approaches, and provide suggestions for researchers constructing their own GT-seq panels. Our GT-seq panel was developed using an ascertainment set consisting of restriction site-associated DNA data from 954 individuals sampled from 23 populations in Minnesota and Wisconsin. We then conducted simulations to test the utility of all loci for parentage analysis and genetic stock identification and designed 600 primer pairs to maximize joint accuracy for these analyses. We conducted three rounds of primer optimization to remove loci that overamplified and our final panel consisted of 436 loci. We also explored different approaches for DNA extraction, multiplexed polymerase chain reaction (PCR) amplification, and cleanup steps during the GT-seq process and discovered the following: (1) inexpensive Chelex extractions performed well for genotyping, (2) the exonuclease I and shrimp alkaline phosphatase (ExoSAP) procedure included in some current protocols did not improve results substantially and was likely unnecessary, and (3) it was possible to PCR amplify panels separately and combine them prior to adapter ligation. Well-optimized GT-seq panels are valuable resources for conservation genetics and our findings and suggestions should aid in their construction in myriad taxa. </p>
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Allen Brain Atlas
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International Brain Laboratory public data
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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.