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2,271 results for “Next generation sequencing”
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: Nonparallelism in MHC IIβ diversity accompanies nonparallelism in pathogen infection of lake whitefish (Coregonus clupeaformis) species pairs as revealed by next generation sequencing
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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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Targeted Next Generation Sequencing data for European Green Crab
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Data from: Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
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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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Utilizing field collected insects for next generation sequencing: effects of sampling, storage, and DNA extraction methods
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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: DNA barcodes from century-old type specimens using next generation sequencing
Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are often more than a century old and have experienced conditions unfavorable for DNA preservation, success in sequence recovery has been uncertain. The present study addresses this challenge by employing next generation sequencing (NGS) to recover sequences for the barcode region of the cytochrome c oxidase 1 gene from small amounts of template DNA. DNA quality was first screened in more than 1800 century-old type specimens of Lepidoptera by attempting to recover 164bp and 94bp reads via Sanger sequencing. This analysis permitted the assignment of each specimen to one of three DNA quality categories – high (164bp sequence), medium (94bp sequence), or low (no sequence). Ten specimens from each category were subsequently analyzed via a PCR-based NGS protocol requiring very little template DNA. It recovered sequence information from all specimens with average read lengths ranging from 458bp to 610bp for the three DNA categories. By sequencing ten specimens in each NGS run, costs were similar to Sanger analysis. Future increases in the number of specimens processed in each run promise substantial reductions in cost, making it possible to anticipate a future where barcode sequences are available from most type specimens.
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.
Data from: Using Illumina Next Generation Sequencing Technologies to sequence multigene families in de novo species
The advent of Next Generation Sequencing Technology (NGST) has revolutionized molecular biology research, allowing for rapid gene/genome sequencing from a multitude of diverse species. As high throughput sequencing becomes more accessible, more efficient workflows must be developed to deal with the amounts of data produced and better assemble the genomes of de novo lineages. We combine traditional laboratory methods with Illumina NGST to amplify and sequence the largest mammalian multigene family, the Olfactory Receptor gene family, for species with and without a reference genome. We develop novel assembly methods to annotate and filter these data, which can be utilized for any gene family or any species. We find no significant difference between the ratio of genes within their respective gene families of our data compared with available genomic data. Using simulated data we explore the limitations of short-read sequence data and our assembly in recovering this gene family. We highlight the benefits and shortcomings of these methods. Compared with data generated from traditional polymerase chain reaction, cloning and Sanger sequencing methodologies, sequence data generated using our pipeline increases yield and sequencing efficiency without reducing the number of unique genes amplified. A cloning step is not required, therefore shortening data generation time. The novel downstream methodologies and workflows described provide a tool to be utilized by many fields of biology, to access and analyze the vast quantities of data generated. By combining laboratory and in silico methods, we provide a means of extracting genomic information for multigene families without complete genome sequencing.
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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.