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126 results for “Extraction Method”
RNA extraction alternative method for SARS-CoV-2 molecular diagnosis
<p>The devastating outbreak of COVID-19 has posed serious challenges for the diagnostics laboratories, often facing global shortage of reagents and equipment. This study aimed at evaluating an additional RNA extraction method respect to those already recommended by WHO and CDC. A new protocol for RNA extraction from nasopharyngeal swab was set up, adapting the Qiagen RNeasy 96 plate for cell lines, and validated on a set of 96 clinical samples analyzed in parallel by a recommended method. The internal control and target genes analysis showed a good agreement between the two extraction methods, indicating that the two approaches can be considered equivalent for the SARS-CoV-2 diagnostics. The addition of this extraction method can help in increasing the throughput for SARS-CoV-2 molecular test, even in a low automation setting.</p> <p>The data set published in Zenodo is the full data analysed in the paper.</p>
Optimising recovery of DNA from minimally-invasive sampling methods: efficacy of buccal swabs, preservation strategy and DNA extraction approaches for amphibian studies_Dataset_Rscript
<p>Datasets and Rscript associated with paper draft titled: "<span>Optimising recovery of DNA from minimally-invasive sampling methods: efficacy of buccal swabs, preservation strategy and DNA extraction approaches for amphibian studies".</span></p> <p> </p> <p>Abstract: <span>Studies in evolution, ecology and conservation are increasingly based on genetic and genomic inferences. With increased focus on molecular approaches, ethical concerns about destructive or more invasive techniques need to be considered, with a push for minimally invasive sampling to be optimised. Buccal swabs have been increasingly used to collect DNA in a number of taxa, including amphibians.<span> </span>However, DNA yield and purity from swabs is often low, limiting its use. In this study we compare different types of swabs, preservation method and storage, and DNA extraction technique in three case studies to assess the optimal approach for recovering DNA in anurans. Out of the five different types of swab that we tested, Isohelix MS-02 and Rapidry swabs generated higher DNA yields than other swabs. When comparing storage buffers, ethanol is a better preservative than a non-alcoholic alternative. Dried samples resulted in similar or better final DNA yields than ethanol-fixed samples if kept cool. DNA extraction via a Qiagen</span><span>™</span><span> DNeasy Blood and Tissue Kit and McHale’s salting out extraction method resulted in similar DNA yields but the Qiagen</span><span>™</span><span> kit extracts contained less contamination. We also found that samples produce better DNA recovery if frozen as soon as possible after collection. We provide recommendations for sample collection and extraction under different conditions, including budgetary considerations, size of individual sampled, access to cold storage facilities, and DNA extraction methodology. Maximising efficacy of all of these factors for better DNA recovery will allow buccal swabs to be used for genetic and genomic studies in a range of vertebrates.</span></p>
Dataset for ''First comparison of MLT 3-dimensional wind retrieval methods and first direct extraction of vertical wind tides''
<p>This dataset supports the figures in the article "First comparison of the MLT vertical wind retrieval methods and first direct extraction of vertical wind tides" and the supporting information. The data are provided in MatLab format.</p>
Data from: Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA
Environmental DNA (eDNA) is used to detect biodiversity by the capture, extraction, and identification of DNA shed to the environment. However, eDNA capture and extraction protocols vary widely across studies. This use of different protocols potentially biases detection results and could significantly hinder a reliable use of eDNA to detect biodiversity. We tested whether choice of eDNA capture and extraction protocols significantly influenced biodiversity detection in aquatic systems. We sampled lake and river water, captured and extracted eDNA using six combinations of different protocols with replication, and tested for the detection of four macroinvertebrate species. Additionally, using the same lake water technical replicates, we compared the effect of capture and extraction protocols on metabarcode detections of biodiversity using 16S for eubacteria and cytochrome c oxidase I (COI) for eukaryotes. Protocol combinations for capture and extraction of eDNA significantly influenced DNA yield and number of sequences obtained from next generation sequencing. We found significantly different detection rates of species ranging from zero percent to thirty-three percent. Differences in which protocol combinations produced the highest metabarcoded biodiversity were detected and demonstrate that different protocols are required for different biodiversity targets. Our results highlight that the choice of molecular protocols used for capture and extraction of eDNA from water can strongly affect biodiversity detection. Consideration of biases caused by choice of protocols should lead to a more consistent and reliable molecular workflow for repeatable and increased detection of biodiversity in aquatic communities.
Data from: HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA
Over the last decade, protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been widely developed. Their use is however limited to DNA of relatively high molecular weight. During the last year, several methods exploiting hybridization capture using probes based on RAD-sequencing loci have circumvented this limitation and opened avenues to the study of samples characterized by degraded DNA, such as historical specimens. Here, we present a major update to those methods, namely Hybridization capture from RAD-derived probes obtained from a reduced eXome template (hyRAD-X), a technique applying RAD-sequencing to messenger RNA from one or few fresh specimens to elaborate bench-top produced probes, i.e., a reduced representation of the exome, further used to capture homologous DNA from a samples set. In contrast to previous hybridization-capture methods, the reference catalog on which reads are aligned does not rely on de novo assembly of anonymous RAD-sequencing loci, but on an assembled transcriptome obtained from RNAseq data, thus increasing the accuracy of loci definition and Single-Nucleotide-Polmorphisms (SNP) call, and targeting, specifically, expressed genes. Finally, the capture step of hyRAD-X relies on RNA probes, increasing stringency of hybridization, making it well suited for low-content DNA samples. As a proof of concept, we applied hyRAD-X to subfossil needles from the coniferous tree Abies alba, collected in lake sediments (Origlio, Switzerland) and dating back from 7200-5800 years before present (BP). More specifically we investigated genetic variation before, during, and after an anthropogenic perturbation that caused an abrupt decrease in Abies alba population size, 6500-6200 years BP. HyRAD-X produced a matrix encompassing 524 exome-derived SNPs. Despite a lower observed heterozygosity was observed during the 6.500-6.200 years BP time slice, genetic composition was nearly identical before and after the perturbation, indicating that re-expansion of the population after the decline was driven by autochthonous specimens. To the best of our knowledge, this is the first time a population genomic study incorporating ancient DNA samples of tree subfossils is conducted at a moderate cost using reproducible exome-reduced complexity.
Data for "A method for intuitively extracting macromolecular dynamics from structural disorder"
<p>Analyses associated with the manuscript "A method for intuitively extracting macromolecular dynamics from structural disorder".</p>
Minerando Motivações para Aplicação de Extract Method: Um Estudo Preliminar
<p>Conjuntos de dados utilizados na pesquisa.</p>
A green method of extracting and recovering flavonoids from Acanthopanax senticosus using deep eutectic solvents
<p><span>In recent years, green extraction of bioactive compounds from herbal medicines has generated widespread interest. Deep eutectic solvents (DES) have widely replaced traditional organic solvents in the extraction process. In this study, the efficiencies of eight tailor-made DESs in extracting flavonoids from <i>Acanthopanax senticosus</i> (AS) were compared. Response surface methodology (RSM) was employed to optimize the influencing parameters including ultrasonic power, HBA-HBD ratio, water content, solid-liquid ratio, extraction temperature and extraction time. DES composed of glycerol and levulinic acid at a 1:1 ratio was established as the most suitable extraction medium. Optimal conditions were ultrasonic power of 500W, water content of 28%, solid-liquid ratio of 1:18 g·mL<sup>-1</sup>, extraction temperature of 55℃ and extraction time of 73 minutes. The extraction yield of AS total flavonoids reached 23.928±0.071 mg·g<sup>-1</sup>, which was 86.3% and 43.8% higher compared with traditional solvent soak and ethanol reflux extraction methods, respectively. Macroporous resin (D-101, HPD-600, S-8 and AB-8) was used to recover flavonoids from extracts. The AB-8 resin showed higher adsorption/desorption performance, with a recovery rate of total flavonoids of up to 71.56±0.256%. In addition, DES solvent could be efficiently recovered through this process and reused. In summary, ultrasonic-assisted DES combined with the macroporous resin enrichment method is exceptionally effective in extracting flavonoids from AS and provides a promising environmentally friendly and recyclable strategy for flavonoid extraction from natural plant sources.</span></p>
Datasets of issue-commit and issue-method links extracted from GitHub repositories
<p>Contains issue-commit and issue-method links extracted from GitHub repositories.</p> <p>Available on GitHub: https://github.com/pragma-once/utilizing-bert-for-traceability/releases</p>
Developing a Method to Automatically Extract Road Boundary and Linear Road Markings from MMS Point Cloud using OBB Collision Detection Techniques
<p>This video demonstrates the application of our method in a software tool for constructing road boundaries and lane marking data.</p>
Development a Method to Extract Antibiotic Concentration From Interstitial Lung and Epithelial Lining Fluid.
ClinicalTrials.gov study NCT03970265. IPD Sharing: NO. Countries: 1. Publications: 1.
A Randomized Parallel-controlled Study Comparing the Ileostomy "Dumpling Suture Method" With Traditional Suture Method in Rectal Anterior Resection Surgery With Specimen Extraction Via Stoma
ClinicalTrials.gov study NCT05985499. IPD Sharing: YES. Countries: 1. Publications: 0.
External Pop Out cs vs Conventional Method for Fetal Head Extraction in Repeatedcaesarean Section.
ClinicalTrials.gov study NCT04968340. IPD Sharing: YES. Countries: 1. Publications: 2.
Data from: A proteomic method to extract, concentrate, digest, and enrich peptides from fossils with colored (humic) substances for mass spectrometry analyses
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Data from: “Direct PCR” optimization yields a rapid, cost-effective, non-destructive, and efficient method for obtaining DNA barcodes without DNA extraction
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Data from: Comparative analysis of DNA extraction methods to study the body surface microbiota of insects: a case study with ant cuticular bacteria
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Data from: Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA
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Data from: Extracting spatio-temporal patterns in animal trajectories: an ecological application of sequence analysis methods
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Data from: HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA
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Utilizing field collected insects for next generation sequencing: effects of sampling, storage, and DNA extraction methods
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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.