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472
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ShareScore release 0.9.0
Dataset results
472 results for “Whole genome sequence”
LeukoSEQ: Whole Genome Sequencing as a First-Line Diagnostic Tool for Leukodystrophies
ClinicalTrials.gov study NCT02699190. IPD Sharing: NO. Countries: 1. Publications: 10.
A Pilot Project Exploring the Impact of Whole Genome Sequencing in Healthcare
ClinicalTrials.gov study NCT01736566. IPD Sharing: Not stated. Countries: 1. Publications: 34.
Study of Ibrutinib in Patients With Symptomatic, Previously Untreated Waldenstrom's Macroglobulinemia, and Impact on Tumor Genomic Evolution Using Whole Genome Sequencing
ClinicalTrials.gov study NCT02604511. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Whole-genome sequencing confirms multiple species of Galapagos giant tortoises
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PacBio whole-genome sequencing and draft assembly of Stentor coeruleus
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A revised phylogeny of Boletaceae using whole genome sequences
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Whole genome sequencing (WGS) data from invasive pine sawfly Diprion similis
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Low-coverage whole genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American Redstart (Setophaga ruticilla)
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Cost-effective library preparation for whole genome sequencing with feather DNA
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Genotypes of Aedes aegypti mosquitoes derived from SNP chip and low-coverage whole genome sequencing for platform cross-validation
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A comparison of phylogenomic inference pipelines for low-coverage whole-genome sequencing in Formica ants
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Data from: Genetic structure and demographic history of house mice in Western Europe inferred using whole genome sequences
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Data from: Whole genome sequencing reveals clade-specific genetic variation in blacklegged ticks
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List of known SNP positions (based on SNP chip data) for base quality score recalibration of alignments for whole-genome resequencing and whole-genome bisulfite sequencing data from great tits (Parus major)
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Data from: Demographic history and inbreeding in two declining sea duck species inferred from whole genome sequence data
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Datasets of "Whole genome sequencing of European autochthonous and commercial pig breeds provides selection signatures of adaptation of genetic resources to different breeding and production systems"
<p>Results of the F<sub>ST</sub> and H<sub>P</sub> analyses.</p>
Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding
<p>Description of 1200bp amplicon primer sets and .bed and .tsv files for SARS-CoV-2 assembly using the ARTIC bioinformatics pipeline.</p>
Data from: Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies
Genomic resources for the domestic dog have improved with the widespread adoption of a 173k SNP array platform and updated reference genome. SNP arrays of this density are sufficient for detecting genetic associations within breeds but are underpowered for finding associations across multiple breeds or in mixed-breed dogs, where linkage disequilibrium rapidly decays between markers, even though such studies would hold particular promise for mapping complex diseases and traits. Here we introduce an imputation reference panel, consisting of 365 diverse, whole-genome sequenced dogs and wolves, which increases the number of markers that can be queried in genome-wide association studies approximately 130-fold. Using previously genotyped dogs, we show the utility of this reference panel in identifying potentially novel associations, including a locus on CFA20 significantly associated with cranial cruciate ligament disease, and fine-mapping for canine body size and blood phenotypes, even when causal loci are not in strong linkage disequilibrium with any single array marker. This reference panel resource will improve future genome-wide association studies for canine complex diseases and other phenotypes.
Whole genome sequence analysis of porcine astroviruses reveals novel genetically diverse genotypes circulating in East African smallholder pig farms
<p>Supplementary materials for the porcine astrovirus study in East Africa.</p> <p><strong>Table S1</strong>: Pairwise comparison of nucleotide sequence identities of the complete (near complete, U460) genomes of the seven (7) astrovirus field strains (bold) and with sequences of other astroviruses available in GenBank </p> <p><strong>Table S2</strong>. Summary of nucleotide sequence identity matrix of the capsid protein (ORF2) among the seven (7) astroviruses field strains (bold) and the known reference strains in the GenBank using Clustal Omega</p> <p><strong>Table S3</strong>. Summary of amino acid sequence identity matrix of the capsid protein (ORF2) among the 7 astroviruses field strains (bold) and the known reference strains in the GenBank using Clustal Omega</p> <p><strong>Table S4</strong>: Estimates of evolutionary divergence between the East African PoAstVs and selected known AstV in the GenBank based on the amino acid sequences of complete ORF2 protein. The number of amino acid differences per site from between sequences is shown. Standard error estimate(s) are shown above the diagonal for our strains.</p> <p><strong>Table S5</strong>. Recommended potential linear antigenic epitopes predicted inside capsid protein (ORF2) of our field strains by SVMTriP web-based tool and corresponding antigenicity predicted by VaxiJen software</p>
An evaluation of inbreeding measures using a whole genome sequenced cattle pedigree
<p>The estimation of the inbreeding coefficient (F) is essential for the study of inbreeding depression (ID) or for the management of populations under conservation. Several methods have been proposed to estimate the realized F using genetic markers, but it remains unclear which one should be used. Here we used whole-genome sequence data for 245 individuals from a Holstein cattle pedigree to empirically evaluate which estimators best capture homozygosity at variants causing ID, such as rare deleterious alleles or loci presenting heterozygote advantage and segregating at intermediate frequency. Estimators relying on the correlation between uniting gametes (F<sub>UNI</sub>) or on the genomic relationships (F<sub>GRM</sub>) presented the highest correlations with these variants. However, homozygosity at rare alleles remained poorly captured. A second group of estimators relying on excess homozygosity (F<sub>HOM</sub>), homozygous-by-descent segments (F<sub>HBD</sub>), runs-of-homozygosity (F<sub>ROH</sub>) or on the known genealogy (F<sub>PED</sub>) was better at capturing whole genome homozygosity, reflecting the consequences of inbreeding on all variants, and for young alleles with low to moderate frequencies. The results indicate that F<sub>UNI</sub> and F<sub>GRM</sub> might present a stronger association with ID. However, the situation might be different when recessive deleterious alleles reach higher frequencies, such as in populations with a small effective population size. For locus specific inbreeding measures or at low marker density, the ranking of the methods can also change as F<sub>HBD </sub>makes better use of the information from neighbouring markers. Finally, we confirmed that genomic measures are in general superior to pedigree-based estimates. In particular, F<sub>PED</sub> was uncorrelated with locus specific homozygosity.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.