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484
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ShareScore release 0.9.0
Dataset results
484 results for “Next-Generation Sequencing”
Data from: Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan
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Data from: Stepwise Threshold Clustering: a new method for genotyping MHC loci using next-generation sequencing technology
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Data from: Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies
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Application of next-generation sequencing for the determination of the bacterial community in the gut contents of brackish copepod species (Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus)
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Data from: "Genome-wide microsatellite marker development from next-generation sequencing of two non-model bat species impacted by wind turbine mortality: Lasiurus borealis and L. cinereus (Vespertilionidae)" in Genomic Resources Notes accepted 1 October 2013 to 30 November 2013
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Utilizing next-generation sequencing to identify prey DNA in western North Atlantic grey seal (Halichoerus grypus) diet
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Data from: Next-generation sequencing for molecular ecology: a caveat regarding pooled samples
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Data from: Parallel tagged next-generation sequencing on pooled samples – a new approach for population genetics in ecology and conservation
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Data from: Targeted next-generation sequencing panels in the diagnosis of Charcot Marie Tooth disease
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Data from: Are Miquihuana rhadiniformis Barr, 1982 and Pseudamara arenaria (LeConte, 1847) (Coleoptera, Carabidae) sphodrines? Phylogenetic analysis of data from next-generation sequencing of museum specimens resolves the tribal-group relationships of these enigmatic taxa
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Data from: Species delimitation in the ground beetle subgenus Liocosmius (Coleoptera: Carabidae: Bembidion), including standard and next-generation sequencing of museum specimens
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Data from: A pragmatic approach to the analysis of diets of generalist predators: the use of next-generation sequencing with no blocking probes
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Data from: Discrimination of grasshopper (Orthoptera: Acrididae) diet and niche overlap using next-generation sequencing of gut contents
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Data from: Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity.
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Data from: Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach
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A method for determining the origin of crude drugs derived from animals using MinION, a compact next-generation sequencer
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Raw sequence of: A comparative analysis of spider prey spectra analyzed through the next-generation sequencing of individual and mixed DNA samples
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Unmasking viral sequences by metagenomic next-generation sequencing in adult human blood samples during steroid-refractory/dependent graft-versus-host disease
<p><b>Background: </b>Viral infections are common complications following allogeneic hematopoietic stem cell transplantation (allo-HSCT<b>)</b>. Allo-HSCT recipients<b> </b>with steroid-refractory/dependent graft-versus-host disease (GvHD) are highly immunosuppressed and are more vulnerable to infections with weakly pathogenic or commensal viruses. Here, twenty-five adult allo-HSCT recipients from 2016 to 2019 with acute or chronic steroid-refractory/dependent GvHD were enrolled in a prospective cohort of patients at Geneva University Hospitals. We performed metagenomics next-generation sequencing (mNGS) analysis using a validated viral pipeline and <i>de novo</i> analysis on pooled stored routine plasma samples collected throughout the period of intensive steroid treatment or second-line GvHD therapy to identify weakly pathogenic, commensal and unexpected viruses.</p> <p><b>Results: </b>Median duration of intensive immunosuppression was 5.1 months (IQR 5.5).<b> </b>GvHD-related mortality rate was 36%.<b> </b>mNGS analysis detected viral nucleotide sequences in 24/25 patients. Sequences of ≥3 distinct viruses were detected in 16/25 patients, <i>Anelloviridae</i> (24/25) and human pegivirus-1 (9/25) were the most prevalent. In 7/25 patients with fatal outcomes, unexpected viral sequences, not assessed by routine investigations, were identified with mNGS and confirmed by RT-PCR. These cases included usutu virus (1), rubella virus (1 vaccine-strain and 1 wild-type), novel human astrovirus (HAstV) MLB2 (1), classic HAstV (1), human polyomavirus 6 and 7 (2), cutavirus (1), and bufavirus (1).</p> <p><b>Conclusions: </b>Unexpected, opportunistic and protracted viral infections were identified in 28% of highly immunocompromised allo-HSCT recipients with steroid refractory/dependent GvHD. These identified viruses have all been previously described in humans, but have poorly understood clinical significance. Rubella virus identification raises the possibility of re-emergence from past infections or vaccinations.</p>
Data from: Diet assessment of the Atlantic Sea Nettle Chrysaora quinquecirrha in Barnegat Bay, New Jersey, using next-generation sequencing
Next generation sequencing (NGS) methodologies have proven useful in deciphering the food items of generalist predators, but have yet to be applied to gelatinous animal gut and tentacle content. NGS can potentially supplement traditional methods of visual identification. Chrysaora quinquecirrha (Atlantic sea nettle) has progressively become more abundant in Mid-Atlantic United States' estuaries including Barnegat Bay (New Jersey), potentially having detrimental effects on both marine organisms and human enterprises. Full characterization of this predator's diet is essential for a comprehensive understanding of its impact on the food web and its management. Here we tested the efficacy of NGS for prey item determination in the Atlantic sea nettle. We implemented a NGS "shotgun" approach to randomly sequence DNA fragments isolated from gut lavages and gastric pouch/tentacle picks of 8 and 84 sea nettles, respectively. These results were verified by visual identification and co-occurring plankton tows. Over 550,000 contigs were assembled from ~110 million paired-end reads. Of these, 100 contigs were confidently assigned to 23 different taxa, including soft bodied organisms previously undocumented as prey species, including copepods, fish, ctenophores, anemones, amphipods, barnacles, shrimp, polychaete worms, flukes, flatworms, echinoderms, gastropods, bivalves, and hemichordates. Our results not only indicate that a "shotgun" NGS approach can supplement visual identification methods, but targeted enrichment of a specific amplicon/gene is not a prerequisite for identifying Atlantic sea nettle prey items.
Data from: De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques.
Next-generation sequencing (NGS) technologies are increasingly applied in many organisms, including non-model organisms that are important for ecological and conservation purposes. Illumina and 454 sequencing are among the most used NGS technologies and have been shown to produce optimal results at reasonable costs when used together. Here, we describe the combined application of these two NGS technologies to characterize the transcriptome of a plant species of ecological and conservation relevance for which no genomic resource is available, Scabiosa columbaria. We obtained 528,557 reads from a 454 GS-FLX run and a total of 28,993,627 reads from two lanes of an Illumina GAII single run. After reads trimming, the de novo assembly of both types of reads produced 109,630 contigs. Both the contigs and the >75 bp remaining singletons were blasted against Uniprot/Swissprot database, resulting in 29,676 and 10,515 significant hits, respectively. Based on sequence similarity with known gene products, these sequences represent at least 12,516 unique genes, most of which are well covered by contig sequences. In addition, we identified 4,320 microsatellite loci, of which 856 had flanking sequences suitable for PCR primer design. We also identified 75,054 putative SNPs. This annotated sequence collection and the relative molecular markers represent a main genomic resource for S. columbaria which should contribute to future research in conservation and population biology studies. Our results demonstrate the utility of NGS technologies as starting point for the development of genomic tools in nonmodel but ecologically important species.
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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.