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2,271 results for “Next generation sequencing”
Next-generation sequencing of AAV.CAP-Mac from Chuapoco et al. (2023) Nature Nanotechnology
<p>Dataset of next-generation sequencing of enrichment of AAV.CAP-Mac in various tissues from the publication:</p> <p>Chuapoco, M.R., Flytzanis, N.C., Goeden, N. <em>et al.</em> Adeno-associated viral vectors for functional intravenous gene transfer throughout the non-human primate brain. <em>Nat. Nanotechnol.</em> (2023). https://doi.org/10.1038/s41565-023-01419-x</p>
Comparative assessment of line-probe assays and targeted next-generation sequencing in drug-resistant tuberculosis diagnosis
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Dataset used for "Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data"
<p>Each simulated dataset was generated using the AbSim R package (version 0.2.6) in a B cell single-lineage fashion. Each B cell clone simulation begins with a random selection from sets of IGHV, IGHD, and IGHJ germline sequences to produce a unique V(D)J recombination event. Then, clones are made by introducing mutations using a local nucleotide context-dependent model (S5F model) along a phylogenetic tree in which branching events occur stochastically. </p>
Next-generation sequencing of newborn screening genes: The accuracy of short-read mapping
<p>We examine the effect of high homology genomic regions on the mapping of genes related to newborn screening while taking different read lengths and patient's ethnic background into consideration.</p>
CusVarDB: A tool for building customized sample-specific variant protein database from Next-generation sequencing datasets
<p>CusVarDB is a windows based tool for creating a variant protein database from Next-generation sequencing datasets. The program supports variant calling for Genome, RNA-Seq and exome datasets.</p> <p>This repository will provide the resultant variant peptides identified in our study and its corresponding information. The detailed information of the table is given below.</p> <p>Supplementary Table 1. This table contains the resultant variant peptides along with its wild-type peptides from BT474, MDMAB157, MFM223, and HCC38 datasets. Along with mutant peptides, this section also provides additional information such as peptide-spectrum match (PSM), Protein accession, cross-correlation value from the search (Xcorr), and retention time (RT).</p> <p>Supplementary Table 2. This table provides the complete details of the resultant peptides. Here the mutant and corresponding wild-type peptides are mentioned in different sheets. For a given mutant peptide its wild-type peptide and corresponding information can be mapped using the VLOOKUP function in Excel by keeping column A (Sl.No) as lookup parameter.</p> <p>Supplementary Table 3. This table briefs about the variants which are already reported in other cancers.</p>
Next-generation Sequencing Data Associated with "Genome Editing Outcomes Reveal Mycobacterial NucS Participates in a Short-Patch Repair of DNA Mismatches"
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Supplementary material Next-generation sequencing reveals that miR-16-5p, miR-19a-3p, miR-451a and miR-25-3p cargo in plasma extracellular vesicles differentiates sedentary young males from athletes.
<p>A sedentary lifestyle is a leading risk factor for global mortality. No objective molecular biomarker of sedentarism is available. Extracellular vesicles miRNAs have been described to respond to exercise. Our aim was to identify the extracellular vesicle miRNA profile of chronically trained young male athletes, endurance and resistance, compared to their sedentary counterparts. A descriptive case-control design with 16 sedentary young men, 16 Olympic male endurance athletes and 16 Olympic male resistance athletes. Next Generation Sequencing and RT-qPCR, external and internal validation, were performed in order to analysed extracellular vesicle miRNA profiles. miR-16-5p, miR-19a-3p and miR-451a were significantly upregulated in SED compared to END and RES. Besides, miR-25-3p was specifically down-regulated in END compared to SED. Extracellular vesicle miR-16-5p, miR-19a-3p, miR-451a provide an objective signature of sedentarism irrespective of the type of exercise and miR-25-3p as a specific responder to endurance training. Therefore, this study provides for the first time an objective measure to categorise individuals as sedentary or trained in young male population and moreover, it highlights a common epigenetic modulation between models of training.</p>
An insight into gill microbiome of Eastern Mediterranean wild fish by applying next generation sequencing
<p>Bacterial diseases of marine fish inflict significant economic damage to fisheries and aquaculture and pose an increasing risk to public health. When addressing fish disease, an accumulating body of research suggests adding another factor to the classic epidemiological triangle of host-environment-pathogen: the microbiome. The gills, being a gateway into the fish body and bearing an important role in fish homeostasis, have been found to be a proxy of the gut microbiota as well as reflecting the microbial communities of surrounding water. In this study, 16S rRNA amplicons of bacterial DNA extracted from the gills of 89 asymptomatic specimens of three wild fish species (<em>Pagrus caeruleostictus, Scomber colias</em> and <em>Saurida lessepsianus</em>) were sequenced using Next Generation Sequencing methodology (NGS). Data analyses revealed the presence of 41 potentially pathogenic species, including several zoonotic agents. Five genera known to include widespread and potentially pathogenic species were chosen for further investigation – <em>Photobacterium, Shewanella, Staphylococcus, Streptococcus</em> and <em>Vibrio</em>. Of these, <em>Photobacterium </em>and <em>Shewanella </em>proved the most prevalent and abundant, making up 30.2% and 11.3% of the Bluespotted seabream (<em>P. caeruleostictus</em>) gill microbiome alone. <em>Photobacterium damselae </em>and <em>Shewanella baltica </em>were most common at the species level. The remaining genera - <em>Vibrio, Staphylococcus</em> and <em>Streptococcus</em> – were less prevalent, and at a species level were comprised of only 1<span>−</span>4% potentially pathogenic representatives. Gill microbiomes exhibited host species specificity, with strong correlations between certain bacterial taxonomic groups. No definite obligatory pathogenic bacteria were found in this study, and it was suggested that pathogenic species are present as either covert pathobionts or as opportunists of the fish found to host them.</p>
Fig. 1 in Marked genetic diversity within Blastocystis in Australian wildlife revealed using a next generation sequencing-phylogenetic approach
Fig. 1. Map showing Melbourne's water catchment areas where samples were collected (2009-2022).
Original NGS dataset from publication "Next-generation sequencing analysis of a cluster of hepatitis C virus infections in a haematology and oncology center".
<p>Original hepatitis C virus hypervariable region 1 NGS sequences in fastq format from patients analyzed in the study "Next-generation sequencing analysis of a cluster of hepatitis C virus infections in a haematology and oncology center". </p> <p> </p>
Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies
<p class="MsoNormal"><strong><u><span>Aim:</span></u></strong><span> Discerning when, where, and how processes of isolation lead to differing biogeography is especially complex for marine species with similar ecological niches and within the same geographic location. We assessed population genetics of congeneric and ecologically similar damselfishes within their overlapping distributions and across potential barriers to geneflow.</span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Taxon:</span></u></strong><span> <em>Dascyllus marginatus </em>(endemic) and <em>Dascyllus abudafur </em>(widespread)<em>.</em></span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Location:</span></u></strong><span> Coral reefs from the Red Sea, Djibouti, Yemen, Oman, and Madagascar. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Methods:</span></u></strong><span> We used RADseq derived SNPs to investigate key differences in population genetics between both species and discuss barriers shaping genetic differentiation (neutral vs. selective) and biogeography. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Results:</span></u></strong><strong><span> </span></strong><em><span>Dascyllus marginatus </span></em><span>inhabited the Red Sea, the coasts of Yemen (including Socotra), and the Gulf of Oman. <em>Dascyllus abudafur</em> species was present from the Red Sea to Madagascar but was absent from Yemen and Oman. Populations of <em>D. marginatus </em>had an order of magnitude higher genetic differentiation compared to <em>D. abudafur</em>, as well as several outlier loci (suggesting selective pressure), which were absent in <em>D. abudafur</em> despite equal sampling locations. In both species, specimens from the Red Sea and Djibouti formed one genetic cluster separated from all other locations. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Main conclusions:</span></u></strong><span> The stronger genetic structure at smaller geographic scale of the endemic species seems associated to faster adaptation to environmental differences; whereas the widespread species only experienced reduced geneflow and neutral differentiation at much larger geographic scales. Restrictive transitions (between the Gulf of Aqaba and the Red Sea or the Red Sea and the Gulf of Aden) did not affect the genetic architecture of either species, while the environmental shift within the Red Sea (at 22°N/20°N) affected the endemic but not the widespread species. Samples from continental Yemen revealed that a genetic break in the Gulf of Aden likely reflects historical colonization processes and not contemporary environmental regimes.</span></p>
Sequences of bacterial and fungal communities by Next-Generation Sequencing (NGS) associated to wall patinas
<p>These data are the DNA sequences obtained from samples of house plaster with chromatic alteration facies. Three areas (VA1, VA3 and VNA6) of the wall were sampled. the DNA was extracted using the Spin Kit For Soil MPBio. </p> <p>The DNA extracts were sequenced by NGS using Illumina MiSeq</p> <p>Two regions were selected V3V5 16S for Bacteria and ITS1 ITS for Fungi. </p>
A next-generation sequencing study of arthropods in the diet of Laysan Teal (Anas laysanensis)
<p><span>The critically endangered Laysan Teal <em>Anas laysanensis</em> (known as koloa pōhaka in the Hawaiian language) in the Northwestern Hawaiian Islands has wild populations on Kamole (Laysan Island), Kuaihelani (Midway Atoll NWR), and Hōlanikū (Kure Atoll). The Laysan Teal faces a new risk on Sand Island, Kuaihelani: non-target poisoning via a pending House Mouse <em>Mus musculus</em> eradication. After mice were observed attacking and depredating Laysan Albatross <em>Phoebastria immutabilis</em> (mōlī) in 2015, plans to eradicate mice were developed to protect this seabird species. However, this approach risks poisoning the Laysan Teal. To reduce exposure, teal will be translocated during mouse eradication. Even so, there is a potential risk of secondary poisoning for teal by ingesting arthropods that feed on mouse bait. We therefore used next-generation sequencing (NGS) to identify which arthropods teal consume. From August 2019 to February 2020, we collected 71 fresh teal faecal samples on Sand Island, and successfully extracted DNA from 21 samples. Via NGS, we found that teal most frequently consume cockroaches (order: Blattodea), freshwater ostracods (Cyprididae), midges (Chironomidae), and isopods (Porcellionidae). To a lesser degree, teal also eat spiders (Araneae), moths (Lepidoptera), beetles (Coleoptera), springtails (Entomobryomorpha), thrips (Thysanoptera), and crabs (Decapoda). Notably, Sand Island's teal consume entirely different arthropods from teal on Kamole, which mainly eat flies (Diptera) and brine shrimp (Anostraca, <em>Artemia </em>sp.). Our study serves as a model for risk mitigation during invasive rodent eradications.</span></p>
Next Generation Sequencing-Based Stratification of Front Line Treatment of HighGrade Neuroendocrine Carcinoma
ClinicalTrials.gov study NCT04452292. IPD Sharing: NO. Countries: 1. Publications: 1.
North Carolina Genomic Evaluation by Next-generation Exome Sequencing, 2
ClinicalTrials.gov study NCT03548779. IPD Sharing: YES. Countries: 1. Publications: 61.
Antibiotic Selection Using Next Generation Sequencing vs Urine Culture
ClinicalTrials.gov study NCT04404855. IPD Sharing: YES. Countries: 1. Publications: 1.
Supplemental data from: Next-generation sequencing base calls for mosaic mutations
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Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies
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Sequences of bacterial and fungal communities by Next-Generation Sequencing (NGS) associated to wall patinas
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Development and application of Faba_bean_130K Targeted Next-Generation Sequencing SNP genotyping platform based on transcriptome sequencing
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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.