Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
130
datasets available to search
ShareScore release 0.7.1
Dataset results
130 results for “whole-genome sequencing”
Fig 4 in Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China
Fig 4. Genome map of Sphingobacterium deserti sp. nov. ZWT. Concentric tracks from the inside to the outside represent the GC nucleotide bias; the GC content; tRNA and rRNA genes on the reverse strand; tRNA and rRNA genes on the forward-strand; reverse-strand coding sequences (CDSs); and forwardstrand CDSs. doi:10.1371/journal. pone.0122254.g004
Fig 1 in Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China
Fig 1. Electron micrograph of the cell morphology of strain ZWT. doi:10.1371/journal.pone.0122254.g001
Fig 5 in Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China
Fig 5. Whole-genome optical mapping barcode of Sphingobacterium deserti sp. nov. ZWT. Vertical lines represent restriction sites; distances between lines represent fragment sizes.
Estimating the rates of adaptive evolution in fungal species using whole-genome sequences - v0.1
<p>GitHub script version v0.1</p>
Cancer Predisposition Testing by Family-based Whole-genome Sequencing (WGS) in Every Child With Newly Diagnosed Cancer
ClinicalTrials.gov study NCT04903782. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow
Open the record for dataset details and reuse information.
Data from: Demographic inference from whole-genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age
Open the record for dataset details and reuse information.
Data from: Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone
Open the record for dataset details and reuse information.
Data from: Next-Gen phylogeography of rainforest trees: measuring landscape-level cpDNA variation from whole-genome sequencing.
Open the record for dataset details and reuse information.
Genotype likelihoods for low-coverage whole-genome sequencing data of yellow warblers
Open the record for dataset details and reuse information.
Low-coverage whole-genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758)
Open the record for dataset details and reuse information.
Data from: Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies
Open the record for dataset details and reuse information.
Data from: High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery
Open the record for dataset details and reuse information.
Data from: Whole-genome sequencing of 128 camels across Asia reveals origin and migration of domestic Bactrian camels
Open the record for dataset details and reuse information.
Simulated data and results from "Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data"
<p>This dataset contains all the simulated data and the results of all the considered methods in the benchmark presented in "Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data" [Zaccaria & Raphael, 2018]. All the data in this dataset and the corresponding formats are fully described at <a href="https://github.com/raphael-group/hatchet-paper">https://github.com/raphael-group/hatchet-paper</a>. The folder <em>simulations</em> which contains the entire dataset has been compressed with standard <em>zip</em>.</p>
Data from: Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery
Premise of the study: We used moderately low-coverage (17×) whole-genome sequencing of Artocarpus camansi (Moraceae) to develop genomic resources for Artocarpus and Moraceae. Methods and Results: A de novo assembly of Illumina short reads (251,378,536 pairs, 2 × 100 bp) accounted for 93% of the predicted genome size. Predicted coding regions were used in a three-way orthology search with published genomes of Morus notabilis and Cannabis sativa. Phylogenetic markers for Moraceae were developed from 333 inferred single-copy exons. Ninety-eight putative MADS-box genes were identified. Analysis of all predicted coding regions resulted in preliminary annotation of 49,089 genes. An analysis of synonymous substitutions for pairs of orthologs (Ks analysis) in M. notabilis and A. camansi strongly suggested a lineage-specific whole-genome duplication in Artocarpus. Conclusions: This study substantially increases the genomic resources available for Artocarpus and Moraceae and demonstrates the value of low-coverage de novo assemblies for nonmodel organisms with moderately large genomes.
Data from: Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole-genome sequencing
The molecular mechanisms and genetic architecture that facilitate adaptive radiation of lineages remain elusive. Polymorphic chromosomal inversions, due to their recombination-reducing effect, are proposed instruments of ecotypic differentiation. Here we study an ecologically diversifying lineage of An. gambiae, known as the Bamako chromosomal form based on its unique complement of three chromosomal inversions, to explore the impact of these inversions on ecotypic differentiation. We used pooled and individual genome sequencing of Bamako, typical (non-Bamako) An. gambiae, and the sister species An. coluzzii to investigate evolutionary relationships and genome-wide patterns of nucleotide diversity and differentiation among lineages. Despite extensive shared polymorphism and limited differentiation from the other taxa, Bamako clusters apart from the other taxa, and forms a maximally supported clade in neighbor-joining trees based on whole genome data (including inversions) or solely on collinear regions. Nevertheless, FST outlier analysis reveals that the majority of differentiated regions between Bamako and typical An. gambiae are located inside chromosomal inversions, consistent with their role in the ecological isolation of Bamako. Exceptionally differentiated genomic regions were enriched for genes implicated in nervous system development and signaling. Candidate genes associated with a selective sweep unique to Bamako contain substitutions not observed in sympatric samples of the other taxa, and several insecticide resistance gene alleles shared between Bamako and other taxa segregate at sharply different frequencies in these samples. Bamako represents a useful window into the initial stages of ecological and genomic differentiation from sympatric populations in this important group of malaria vectors.
Data from: Whole-genome sequencing approaches for conservation biology: advantages, limitations, and practical recommendations
Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved (huWGR) or resolved haplotypes (hrWGR), the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq), and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in non-model species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons, and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g. structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently though, no single WGR approach fulfills all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many non-model species and fields including conservation biology.
Supplementary Material for Ph.D. thesis: "Development of a data-intensive centralized system for surveillance and outbreak investigation of bacterial pathogens using whole-genome sequencing""
<p>Supplementary material for Ph.D. thesis.</p>
Transposase-Assisted Tagmentation: An Economical and Scalable Strategy for Single-Worm Whole-Genome Sequencing (other species)
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
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.