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2,785 results for “genotyping”
Transgenerational plasticity of dispersal-related traits in a ciliate: genotype-dependency and fitness consequences
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Data from: Nitrogen availability and plant-plant interactions drive leaf silicon concentration in wheat genotypes
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Microsatellite genotypes, cluster membership and metadata of Central European wolves (Canis lupus)
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Differential impact of nevirapine on artemether-lumefantrine pharmacokinetics in individuals stratified by CYP2B6 c.516G>T genotypes
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Association of physical activity and APOE genotype with longitudinal cognitive change in early PD
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Field data and microsatellite genotypes of Cercidiphyllum japonicum
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Data from: Progeny contribution scores in offense double-matings of different genotypes for the Sdic region
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Microsatellite genotypes and extraction plate positions from publication: Genetic structure across urban and agricultural landscapes reveals evidence of resource specialization and philopatry in the Eastern carpenter bee, Xylocopa virginica L.
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Genotype reference database (GRDB) for Alouatta caraya
<p>The black and gold howler monkey (<em>Alouatta caraya</em>) is a neotropical primate that faces the highest capture pressure for illegal trade in Argentina. Here, present a Genotype reference database (GRDB) this species. Overall, we were able to correctly assign 73% of the individuals in the database to nearest population of origin, and 93.3% to their cluster of origin. </p>
Genotypes, variants and pedigree from a human parent-offspring trio (NA12878)
<p>This dataset includes whole genome sequencing data, produced at the French National Research Center for Human Genomics (CNRGH), with known pedigree information:<br> - The VCF file contains genotypes and variants from a CEU parent-offspring trio comprising NA12878 (child), NA12891 (father) and NA12892 (mother).<br> For each member, 150-bp paired-end whole genome sequencing data were generated on the Illumina HiSeq X system, from a PCR-free library (40x).<br> - The TFAM file contains pedigree information of this CEU parent-offspring trio.</p>
Data from: More affordable and effective noninvasive SNP genotyping using high-throughput amplicon sequencing
<p>Non-invasive genotyping methods have become key elements of wildlife research over the last two decades, but their widespread adoption is limited by high costs, low success rates, and high error rates. <span>The information lost when genotyping success is low may lead to decreased precision in animal population densities, which could misguide conservation and management actions.</span> <span>Single nucleotide polymorphisms (SNPs) provide a promising alternative to traditionally used microsatellites as SNPs allow amplification of shorter DNA fragments, are less prone to genotyping errors, and produce results that are easily shared among laboratories.</span> Here, we outline a detailed protocol for cost-effective and accurate noninvasive SNP genotyping using multiplexed amplicon sequencing optimized for degraded DNA. <span>We validated this method for individual identification by genotyping 216 scats, 18 hairs and 15 tissues from coyotes (<i>Canis latrans</i>) using 26 SNPs. </span><a name="_Hlk33181599">Our genotyping success rate for scat samples was 93%, and 100% for hair and tissue, representing a substantial increase compared to previous microsatellite-based studies while remaining at a low cost of under $5 per PCR replicate (excluding labor). </a>The accuracy of the genotypes was further corroborated in that genotypes from scats matching known, GPS-collared coyotes were always located within the territory of the known individual. We also show that different levels of multiplexing produced similar results, but that PCR product cleanup strategies can have substantial effects on genotyping success. By making noninvasive genotyping more affordable, accurate, and efficient, this research may allow for a substantial increase in the use of noninvasive methods to monitor and conserve free-ranging wildlife populations.</p>
Individual genotypes of 1 416 brook trout genotyped at 14 779 high-quality SNPs for studying local adaptation and maladaptation in small populations
<p><span><span><span><span><span><span><span><span><span><span><span>Investigating the relative importance of neutral <i>versus</i> selective processes governing the accumulation of genetic variants is a key goal in both evolutionary and conservation biology. This is particularly true in the context of small populations, where genetic drift can counteract the effect of selection. Using Brook Charr (<i>Salvelinus fontinalis</i>) from Québec, Canada as a case study, we investigated the importance of demographic <i>versus</i> selective processes governing the accumulation of both adaptive and maladaptive mutations in closed <i>versus</i> open and connected populations to assess gene flow effect. This was achieved by using 14 779 high-quality filtered SNPs genotyped among 1 416 fish representing 50 populations from three life history types: lacustrine (closed populations), riverine and anadromous (connected populations). Using the Provean algorithm, we observed a considerable accumulation of putative deleterious mutations across populations. The absence of correlation between the occurrence of putatively beneficial or deleterious mutations and local recombination rate supports the hypothesis that genetic drift might be the main driver of the accumulation of such variants. However, despite a lower genetic diversity observed in lacustrine than in riverine or anadromous populations, lacustrine populations do not exhibit more deleterious mutations than the two other history types, suggesting that the negative effect of genetic drift in lacustrine populations may be mitigated by that of relaxed purifying selection. Moreover, we also identified genomic regions associated with anadromy, as well as an overrepresentation of transposable elements associated with variation in environmental variables, thus supporting the importance of transposable elements in adaptation. </span></span></span></span></span></span></span></span></span></span></span></p>
CRC tumor profiled in Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling
<p>Plain text files from mgatk output of CRC tumor sample originally described in "Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling" (https://doi.org/10.1038/s41587-020-0645-6). </p>
Selected data for Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling
<p>TF1 cell line (Figure 3) and CRC cancer (Figure 4) data from the "Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling" work. </p>
Data from: Variant files for genotypic and sex-reversed males
<p>X and Y chromosomes are usually derived from a pair of homologous autosomes, which then diverge from each other over time. Although Y-specific features have been characterized in sex chromosomes of various ages, the earliest stages of Y chromosome evolution remain elusive. In particular, we do not know whether early stages of Y chromosome evolution consist of changes to individual genes or happen via chromosome-scale divergence from the X. To address this question, we quantified divergence between young proto-X and proto-Y chromosomes in the house fly, <i>Musca domestica</i>. We compared proto-sex chromosome sequence and gene expression between genotypic (XY) and sex-reversed (XX) males. We find evidence for sequence divergence between genes on the proto-X and proto-Y, including five genes with mitochondrial functions. There is also an excess of genes with divergent expression between the proto-X and proto-Y, but the number of genes is small. This suggests that individual proto-Y genes, but not the entire proto-Y chromosome, have diverged from the proto-X. We identified one gene, encoding an axonemal dynein assembly factor (which functions in sperm motility), that has higher expression in XY males than XX males because of a disproportionate contribution of the proto-Y allele to gene expression. The up-regulation of the proto-Y allele may be favored in males because of this gene's function in spermatogenesis. The evolutionary divergence between proto-X and proto-Y copies of this gene, as well as the mitochondrial genes, is consistent with selection in males affecting the evolution of individual genes during early Y chromosome evolution.</p>
Data from: Ecology shapes epistasis in a genotype-phenotype-fitness map for stick insect colour
<p>Genetic interactions such as epistasis are widespread in nature and can shape evolutionary dynamics. Epistasis occurs due to non-linearity in biological systems, which can arise via cellular processes that convert genotype to phenotype and via selective processes that connect phenotype to fitness. Few studies in nature have connected genotype to phenotype to fitness for multiple potentially interacting genetic variants. Thus, the causes of epistasis in the wild remain poorly understood. Here, we show that epistasis for fitness is an emergent and predictable property of non-linear selective processes. We do so by measuring the genetic basis of cryptic colouration and survival in a field experiment with stick insects. We find that colouration exhibits a largely additive genetic basis, but with some effects of epistasis that enhance differentiation between colour morphs. In terms of fitness, different combinations of loci affecting colouration confer high survival in one host-plant treatment. Specifically, non-linear correlational selection for specific combinations of colour traits in this treatment drives the emergence of pairwise and higher-order epistasis for fitness at loci underlying colour. In turn, this results in a rugged fitness landscape for genotypes. In contrast, fitness epistasis was dampened in another treatment, where selection was weaker. Patterns of epistasis that are shaped by ecologically based selection could be common, and central to understanding fitness landscapes, the dynamics of evolution, and potentially other complex systems.</p>
Genotype data and analysis code for HDY-20-A0076RR
<p>Selection pressure from parasites is thought to be a major force shaping the extreme polymorphism of the major histocompatibility complex (MHC) genes, but the modes and consequences of selection remain unclear. Here, we analyse MHC class II and microsatellite diversity in 16 guppy (<i>Poecilia reticulata</i>) populations from two islands (Trinidad and Tobago) that have been separated for at least 10 ky. Within-population MHC diversity was high, but allele sharing was limited within islands and even lower between islands, suggesting relatively fast turnover of alleles. Allelic lineages strongly supported in phylogenetic analyses tended to be island-specific, suggesting rapid lineage sorting, and an expansion of an allelic lineage private to Tobago was observed. New alleles appear to be generated locally at a detectably high frequency. We did not detect a consistent signature of local adaptation, but F<sub>ST</sub> outlier analysis suggested that balancing selection may be the more general process behind spatial variation in MHC allele frequencies in this system, particularly within Trinidad. We found no evidence for divergent allele advantage within populations, or for decreased genetic structuring of MHC supertypes compared to MHC alleles. The dynamic and complex nature of MHC evolution we observed in guppies, coupled with some evidence for balancing selection shaping MHC allele frequencies, are consistent with Red Queen processes of host-parasite coevolution.</p>
Genotype count for all coding variants in type I IFN genes investigated in 659 life-threatening COVID-19 patients and 534 asymptomatic/mild infected controls
<p>Clinical outcome upon infection with SARS-CoV-2 ranges from silent infection to lethal COVID-19. We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern TLR3- and IRF7-dependent type I interferon (IFN) immunity to influenza virus, in 659 patients with life-threatening COVID-19 pneumonia, relative to 534 subjects with asymptomatic or benign infection. By testing these and other rare variants at these 13 loci, we experimentally define LOF variants in 23 patients (3.5%), aged 17 to 77 years, underlying autosomal recessive or dominant deficiencies. We show that human fibroblasts with mutations affecting this pathway are vulnerable to SARS-CoV-2. Inborn errors of TLR3- and IRF7-dependent type I IFN immunity can underlie life-threatening COVID-19 pneumonia in patients with no prior severe infection.</p>
Supplementary Information for: A cautionary note on the use of genotype callers in phylogenomics
<p>Next-generation-sequencing genotype callers are commonly used in studies to call variants from newly-sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional genotype callers, such as the one from GATK, is that they are optimized for variant calling at the population level. However, when these callers are used at the phylogenetic level, the consequences for downstream analyses can be substantial. Here, we performed simulations to compare the performance between the genotype callers of GATK and ATLAS, and present their differences at various phylogenetic scales. We show that the genotype caller of GATK substantially underestimates the number of variants at the phylogenetic level, but not at the population level. We also found that the accuracy of heterozygote calls declines with increasing distance to the reference genome. We quantified this decline, and found that it is very sharp in GATK, while ATLAS maintains a high accuracy even at moderately-divergent species from the reference. We further suggest that efforts should be taken towards acquiring more reference genomes per species, before pursuing high-scale phylogenomic studies.</p>
Multi-locus microsatellite genotypes of Pocillopora acuta (Scleractinia: Pocilloporidae) in the Bolinao-Anda Reef Complex, Philippines
<p>This repository contains genotype data and sampling metadata used for the manuscript "Shifts in coral clonality along a gradient of disturbance: insights on reproduction and dispersal of <em>Pocillopora acuta</em>". The dataset contains genotypes of 428 <em>P. acuta </em>colonies using 16 polymorphic microsatellite loci, colony sizes, in-transect locations of each coral, and geographic coordinates of reef sites. These were used to examine clonal richness and structure, population genetic differentiation, and demographic and genetic connectivity within the reef system. In the study, we estimated the relative contribution of sexual and asexual modes of reproduction to population maintenance, and inferred the species' spatial scale of realized dispersal all against a backdrop of varying levels of wave exposure. </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.