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6 results for “BARCODE standard”
Data from: Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity
<p>A repository containing the data and R code for the associated manuscript titled "Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity"</p> <p>Created by Romana K. Salis</p> <div> <h2>Content Overview</h2> <a href="https://github.com/rksalis/LNU_insectbarcoding/tree/main#content-overview"></a></div> <div> <h3>Rcode:</h3> <a href="https://github.com/rksalis/LNU_insectbarcoding/tree/main#rcode"></a></div> <p>analysis_070923.R</p> <div> <h3>Data files:</h3> <a href="https://github.com/rksalis/LNU_insectbarcoding/tree/main#data-files"></a></div> <p>literature_search_210624.csv barcoding_datasets.csv - barcoding datasets match category counts for the butterflies, bees and wasps</p> <p>barcoding_VB_thresholds.csv - barcoding datasets match category counts for the vietnamese butterfly with different similarity thresholds</p> <p>barcoding_VB_families.csv - barcoding datasets match category counts for the vietnamese butterfly families</p> <p>vietkordfinal_x.csv - intraspecific similarity and geographic distance</p> <p>vietnam_area.csv - intraspecific similarity and sampling area</p> <p>BINsvSp.csv - number of BINs and morphospecies</p> <p>Metabarcoding_Results_CommonSpecies.csv - metabarcoding results including the species only those also identified by morphology</p> <p>Metabarcoding_Results_BINSpecies.csv - metabarcoding results BIN species</p> <p>Metabarcoding_Results_BINs.csv - metabarcoding results all BINs</p>
Data from: DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity
Documenting the diversity of marine life is challenging because many species are cryptic, small, and rare, and belong to poorly known groups. New sequencing technologies, especially when combined with standardized sampling, promise to make comprehensive biodiversity assessments and monitoring feasible on a large scale. We used this approach to characterize patterns of diversity on oyster reefs across a range of geographic scales comprising a temperate location [Virginia (VA)] and a subtropical location [Florida (FL)]. Eukaryotic organisms that colonized multilayered settlement surfaces (autonomous reef monitoring structures) over a 6-mo period were identified by cytochrome c oxidase subunit I barcoding (>2-mm mobile organisms) and metabarcoding (sessile and smaller mobile organisms). In a total area of ∼15.64 m2 and volume of ∼0.09 m3, 2,179 operational taxonomic units (OTUs) were recorded from 983,056 sequences. However, only 10.9% could be matched to reference barcodes in public databases, with only 8.2% matching barcodes with both genus and species names. Taxonomic coverage was broad, particularly for animals (22 phyla recorded), but 35.6% of OTUs detected via metabarcoding could not be confidently assigned to a taxonomic group. The smallest size fraction (500 to 106 μm) was the most diverse (more than two-thirds of OTUs). There was little taxonomic overlap between VA and FL, and samples separated by ∼2 m were significantly more similar than samples separated by ∼100 m. Ground-truthing with independent assessments of taxonomic composition indicated that both presence–absence information and relative abundance information are captured by metabarcoding data, suggesting considerable potential for ecological studies and environmental monitoring.
Data from: DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity
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Data from: DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples
Although species assignment of scats is important to study carnivoran biology, there is still no standardized assay for the identification of carnivores worldwide, which would allow large-scale routine assessments and reliable cross-comparison of results. Here we evaluate the potential of two short mtDNA fragments (ATP6 [126 bp] and COI [187 bp]) to serve as standard markers for the Carnivora. Samples of 66 species were sequenced for one or both of these segments. Alignments were complemented with archival sequences, and analyzed with three approaches (tree-based, distance-based and character-based). Intraspecific genetic distances were generally lower than between-species distances, resulting in diagnosable clusters for 86% (ATP6) and and 85% (COI) of the species. Notable exceptions were recently diverged species, most of which could still be identified using diagnostic characters, uniqueness of haplotypes, or by reducing the geographic scope of the comparison. In silico comparative analyses were also performed with a 110-bp cytochrome b (cytb) segment, whose identification success was lower (70%), possibly due to the smaller number of informative sites and/or the influence of misidentified sequences obtained from GenBank. Finally, we performed case-studies with faecal samples, which supported the suitability of our two focal markers for poor-quality DNA, and allowed an assessment of prey-DNA co-amplification. No evidence of prey DNA contamination was found for ATP6, while some cases were observed for COI and subsequently eliminated by the design of more specific primers. Overall, our results indicate that these segments hold good potential as standard markers for accurate species-level identification in the Carnivora.
Data from: DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples
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CRISPR Anchor screening of a barcoded library in cells treated with standard of care neuroblastoma drugs
GEO Series GSE223991. Homo sapiens. 202 samples. Type: Other.
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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.