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484 results for “Next-Generation Sequencing”
A method for determining the origin of crude drugs derived from animals using MinION, a compact next-generation sequencer
<p><span>We evaluated whether MinION, an inexpensive, portable sequencer, can be applied for identifying the origin of crude drugs</span> <span>derived from animals</span><span>.</span><span> Standard and nonstandard crude drugs with different species of origin were examined. In addition, the standards mixed with nonstandard samples </span><span>were used</span><span>.</span><span> As a target gene, cytochrome c oxidase I was amplified and sequenced. The Fast mode results had a slightly lower match ratio than High-accuracy mode, but the animals of origin were correctly determined by BLAST for all samples. For antler velvet derived from <em>Rangifer tarandus</em>, even the sequences were aligned based on <em>Cervus elaphus</em>, the animal of origin was determined correctly. Minor contents could be detected from mixtures of two animals, if the mixtures contained at least 19:1 mtDNA when the coverage allele-fraction threshold was 0.05. By contrast, in Fast mode, two sequences could not be separated due to the low accuracy of the base-calling in each read. For field work, the species of origin of crude drugs could be identified, by only simple DNA extraction and library preparation. Therefore, MinION appears to be a convenient tool for identifying the origin of crude drugs derived from animals.</span></p>
Data from: Stepwise Threshold Clustering: a new method for genotyping MHC loci using next-generation sequencing technology
Genes of the vertebrate major histocompatibility complex (MHC) are of great interest to biologists because of their important role in immunity and disease, and their extremely high levels of genetic diversity. Next generation sequencing (NGS) technologies are quickly becoming the method of choice for high-throughput genotyping of multi-locus templates like MHC in non-model organisms. Previous approaches to genotyping MHC genes using NGS technologies suffer from two problems: 1) a "gray zone" where low frequency alleles and high frequency artifacts can be difficult to disentangle and 2) a similar sequence problem, where very similar alleles can be difficult to distinguish as two distinct alleles. Here were present a new method for genotyping MHC loci – Stepwise Threshold Clustering (STC) – that addresses these problems by taking full advantage of the increase in sequence data provided by NGS technologies. Unlike previous approaches for genotyping MHC with NGS data that attempt to classify individual sequences as alleles or artifacts, STC uses a quasi-Dirichlet clustering algorithm to cluster similar sequences at increasing levels of sequence similarity. By applying frequency and similarity based criteria to clusters rather than individual sequences, STC is able to successfully identify clusters of sequences that correspond to individual or similar alleles present in the genomes of individual samples. Furthermore, STC does not require duplicate runs of all samples, increasing the number of samples that can be genotyped in a given project. We show how the STC method works using a single sample library. We then apply STC to 295 threespine stickleback (Gasterosteus aculeatus) samples from four populations and show that neighboring populations differ significantly in MHC allele pools. We show that STC is a reliable, accurate, efficient, and flexible method for genotyping MHC that will be of use to biologists interested in a variety of downstream applications.
Supplementary material 1 from: Yuhui X, Lijun Z, Yue H, Xiaoqi W, Chen Z, Huilun Z, Ruoran W, Da P, Hongying S (2017) Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order (Brachyura, Potamidae). ZooKeys 705: 41-60. https://doi.org/10.3897/zookeys.705.11852
Figure S1 : Explanation note: Comparisons of the consensus sequence and variable sites in the entire mNCR for Sinopotamon yaanense, S. yangtsekiense and S. xiushuiense. The conserved central domain is grey shaded, and the extended termination associated sequences (ETAS) is underlined.
Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery
<p>This repository contains data and code used to analyze data for this manuscript: </p> <p><em>Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery</em></p>
FIGURE 2 in USING Next-Generation Sequencing (NGS) TO UNCOVER DIVERSITY OF WOOD-DECAYING FUNGI IN NEOTROPICAL ATLANTIC FORESTS
FIGURE 2. Relative abundances of reads of fungal genera per study area and metabarcode using 95% sequence similarity with reference sequences in the UNITE database as surrogate for traditional taxonomic generic concepts.
FIGURE 1 in USING Next-Generation Sequencing (NGS) TO UNCOVER DIVERSITY OF WOOD-DECAYING FUNGI IN NEOTROPICAL ATLANTIC FORESTS
FIGURE 1. Genera richness at the levels of phylum, class and order per study area and metabarcode using 95% sequence similarity with reference sequences in the UNITE database as surrogate for traditional taxonomic generic concepts.
A Worldwide Cancer Registry Enrolling Participants Profiled With a Next-Generation Sequencing Test
ClinicalTrials.gov study NCT04529122. IPD Sharing: YES. Countries: 32. Publications: 1.
Next-Generation Sequencing Diagnostics of Bacteremia in Sepsis
ClinicalTrials.gov study NCT03356249. IPD Sharing: NO. Countries: 1. Publications: 3.
Metagenomic Next-Generation Sequencing for the Diagnosis of Fracture-related Infection
ClinicalTrials.gov study NCT07256405. IPD Sharing: NO. Countries: 1. Publications: 5.
Metagenomic Next-Generation Sequencing Guides Anti-Infection Strategies
ClinicalTrials.gov study NCT06145841. IPD Sharing: NO. Countries: 1. Publications: 3.
To Investigate the Molecular Mechanism of Traditional Chinese Medicine Constitution Using Next-generation Sequencing in Nasopharyngeal Carcinoma
ClinicalTrials.gov study NCT03578575. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Biodiversity assessment using next-generation sequencing: comparison of phylogenetic and functional diversity between Nebraska grasslands
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Data from: Exploring evolution and diversity of Chinese Dipterocarpaceae using next-generation sequencing
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Data from: The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing
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Data from: Next-generation sequencing for rodent barcoding: species identification from fresh, degraded and environmental samples
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Data from: Two new phragmotic ant species from Africa: morphology and next-generation sequencing solve a caste association problem in the genus Carebara Westwood
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Data from: Development of genomic resources for Nothofagus species using next-generation sequencing data
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Data from: Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform
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Data from: A next-generation sequencing approach to river biomonitoring using benthic diatoms
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Data from: Sequence capture and next-generation sequencing of ultraconserved elements in a large-genome salamander
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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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.