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143 results for “DNA extraction”
Evaluation of an adapted semi-automated DNA extraction for human salivary shotgun metagenomics
<p>This deposit contains :</p> <p>- a RMarkdown filte containing the codes for the mcirobial analysis of saliva samples</p> <p>- the html report with codes, results and figures</p> <p>- a RData containing microbial datasets (MSp species abundance table, genus, family and phylum abundance tables, matrix of genes correlations, taxonomy)</p> <p>- a RData containing associated metadata </p>
NEON Biorepository Soil Microbe Collection (DNA Extracts ) (repackaging of occurrences published by the NEON Biorepository Data Portal)
This collection contains genetic extracts from soil microbes collected during periodic soil sampling at NEON terrestrial sites (NEON sample class: mic_dnaExtraction_in.soilDnaSampleID). Three unique locations are sampled per plot with ten soil plots per site. Bouts occur three times per year in order to capture the prevailing conditions at the site during different seasons, except in Alaska where there only 1 bout is possible. However, the frequency of genetic analysis and thus DNA archiving varies by site type. Soil sampling is conducted to a maximum depth of 30 ± 1 cm, and when organic (O) and mineral (M) horizons are present within a single profile, they are separated prior to analysis and archiving. However, other sub-horizons are not separated. During the majority of bouts, only the top horizon (O if present, else M) is analyzed for genetic content. Soils are homogenized and non-soil material is removed by hand in the field, then subsamples are immediately frozen on dry ice. They are maintained in ultra-low temperature freezers until they are shipped to an analytical facility for DNA extraction, sample preparation and sequencing. During peak greenness bouts, subsamples from each of the 3 sampling locations per plot are combined to form a plot-level composite that is used for metagenomics analysis. Laboratory metadata are delivered to NEON for QC testing and acceptance, and then formatted for upload to public sequence repositories. Genetic extracts are shipped from the analytical facility in 96-well plates to the NEON Biorepository to be archived at -80 degrees Celsius. See links below for NEON data products that provide physical, chemical, and biological measurements for these same soils (soil pH, moisture, and microbial properties are always measured; chemical properties are determined only for a subset of collection bouts). The metabarcoding protocol used by Battelle Applied Genomics is available in the NEON document library (https://data.neonscience.org/docu
All raw data for Fukuzawa, T et al. "Environmental DNA extraction method for a high and stable DNA yield"
<p>The all raw data of quantitative PCR for environmental DNA in Fukuzawa, T et al. "Environmental DNA extraction method for a high and stable DNA yield".</p> <p> </p>
Extracting abundance information from DNA-based data
<p><span><span><span><span>The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to the reconstruction of diets and quantitative foodwebs, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, capture bias, capture noise, species pipeline biases, and pipeline noise all combine to inject error into DNA-based datasets. This review focuses on methods for correcting the latter two error sources, as the first two are addressed extensively in the ecological survey literature. To extract abundance information from DNA-based data, it is useful to distinguish two concepts. (1) <em>Across</em>-species quantification describes relative species abundances within a single sample. (2) In contrast, <em>within</em>-species quantification describes how the abundance of each individual species varies across samples, where the samples could be a time series, an environmental gradient, or different experimental treatments. In the first part of this paper, we review methods to remove species pipeline biases and pipeline noise. In the second part, we provide a detailed protocol and demonstrate experimentally how to use a 'DNA spike-in' (an internal standard) to remove pipeline noise and recover within-species abundance information.</span></span></span></span></p>
Evaluation of DNA extracted from timber rattlesnake (Cotalus horridus) cloacal and blood swabs for microsatellite genotyping
<p>Genetic research is a key component to modern wildlife conservation, but it is contingent on the collection of reliable and high-quality genetic samples. Invasive genetic sampling techniques have potential to negatively impact individuals, which may be prohibitive when working with threatened and endangered species. Prior to sample collection, project managers must try to balance the negative impact on individuals included in the study with the demand for DNA and the difficulty of obtaining samples. Although established methods for blood and tissue collection in reptiles meet the need for high-quantity and quality DNA, they inherently require longer handling times and more skill to obtain. Thus, non-invasive DNA collection methods, such as cloacal swabs, may be preferred when animal welfare is a priority. Cloacal swabs are quicker, easier, require less training and reduce handling time. To evaluate cloacal swabbing as an alternative to collecting blood, we obtained both cloacal and blood swabs. We extracted DNA from cloacal and blood cells that were collected from 23 Timber Rattlesnakes (Crotalus horridus). We assessed DNA by purity (A260/A280), concentration, and microsatellite genotyping. Our results show high-quality DNA can be obtained from both cloacal swabs and blood samples, but quality and concentration of DNA was significantly lower from cloacal swabs. Further, degradation and contamination affects the performance of cloacal DNA when compared to blood DNA in microsatellite-based genotyping. Although we recommend collecting blood samples whenever possible to obtain the highest-quality DNA, cloacal swabs represent a viable alternative for genetic sampling when using microsatellite loci as genetic markers.</p>
Figure 4 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases
Figure 4. Identification of PCR inhibitors in 18 biological samples positive for Aspergillus. Graph A: Ct values obtained from pure and diluted DNA samples (dilution rate 1/20). Graph B: Ct values obtained with 20 copies of a plasmid DNA systematically added to the same biological samples (undiluted and diluted) and a negative control sample (NC).
Figure 2 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases
Figure 2. Influence of proteinase K digestion (56 °C overnight) on DNA extraction. Graph A shows the Ct values obtained by quantifying THP1 cell DNA derived from direct extraction with the NucliSENS easyMAG system and extraction performed on the same quantity of cells following overnight (ON) digestion with Proteinase K. Graph B shows Leishmania quantification after extraction with the NucliSENS easyMAG system both with and without PK and quantification after extraction using a QIAamp DNA Mini kit after ON digestion with PK.
Figure 7 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases
Figure 7. Variation of the ratio between kinetoplastic DNA and nuclear DNA extraction with various Leishmania quantities in the presence of 103 THP1 cells.
Figure 5 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases
Figure 5. Yield of DNA extraction from Leishmania and THP1 cells using the NucliSENS easyMAG system.
Figure 3 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases
Figure 3. Results of the extraction experiments performed on yeast (Candida albicans) and filamentous fungi (Aspergillus fumigatus). A presents the kinetics of the extraction process after vortexing and glass-bead treatment. B shows the differences in DNA quantity obtained from fungal cells using the FastPrep system (with) compared to the same process without grinding.
Figure 6 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases
Figure 6. Influence of the quantity of human cells (THP1 cells) on Leishmania quantification at various concentrations of host cells and parasites.
Fig. 2 in Protocol Optimization For Genomic Dna Extraction And Rapd-Pcr Of Alien Ponto-Caspian Amphipod Pontogammarus Robustoides
Fig. 2. RAPD fingerprints results from different samples of Pontogammarus robustoides with primers OPA-02 (1-12 runners- different samples of Pontogammarus robustoides; K- control) using RAPD-PCR 10 × Taq buffer with KCl.
Fig. 1 in Callicultureinducingfromredclover(Trifolium Pratense L.) Wild Accessions And Results Of Dna Extraction
Fig. 1. Results of flow cytometry: a) 2n ploidy control, b) the typical result for leaves, c) the typical result for stems, d) the typical result for roots.
Fig. 3. Agarose gel image Fig. 4 in Optimization Of Dna Extraction Protocol For Dna Isolation From Air-Dried Collection Material For Further Phylogenetic Analysis (Coleoptera: Carabidae)
Fig. 3. Agarose gel image Fig. 4. Agarose gel image (successful PCR amplification) (failed PCR amplification) M: marker (bp) M: marker (bp) A1: Agonum fuliginosum Panzer, 1809 A: Agonum fuliginosum Panzer, 1809 A2: Agonum thoreyi Dejean, 1828 O: Omophron aequale aequale Morawitz, 1863 O: Omophron aequale aequale Morawitz, 1863 N: Notiophilus semistriatus Say, 1823 N: Notiophilus semistriatus Say, 1823 Nk: negative control. Nk: negative control.
Fig. 1 in Optimization Of Dna Extraction Protocol For Dna Isolation From Air-Dried Collection Material For Further Phylogenetic Analysis (Coleoptera: Carabidae)
Fig. 1. Photo of Omophron aequale jacobsoni Fig. 2. Photo of Omophron aequale jacobsoni Semenov, 1922 before incubation. Semenov, 1922 after 16 h (56°C) incubation time in tissue lysis buffer with proteinase K.
Fig. 2 in Optimisation Of Dna Extraction And Rapd-Pcr Amplification For Population Genetic Analysis Of Daphnia Cucullata Sars, 1862 (Crustacea: Cladocera)
Fig. 2. RAPD fingerprints results from different samples of Daphnia cucullata with primers OPA-03 and OPA-05 (M- marker, 1-11 runners- different samples of Daphnia cucullata; 12- control) using RAPD-PCR 10 × Taq buffer with (NH4)2SO4.
Fig.1 in Optimisation Of Dna Extraction And Rapd-Pcr Amplification For Population Genetic Analysis Of Daphnia Cucullata Sars, 1862 (Crustacea: Cladocera)
Fig.1. RAPD fingerprints results from different samples of Daphnia cucullata with primers OPA-03 and OPA-05 (M- marker, 1-16 runners- different samples of Daphnia cucullata; 17- control) using RAPD-PCR 10 × Taq buffer with KCl.
Figure 1. DNA extraction with two different protocols from different noninvasive samples. Lines 1, 3, 5 in Evaluation of methods for molecular sex-typing of three heron species from different DNA sources
Figure 1. DNA extraction with two different protocols from different noninvasive samples. Lines 1, 3, 5, and 7: DNA extraction with commercial kit; Lines 2, 4, 6, and 8: DNA extracted with modified standard protocol. Lines 1–2: eggshells (Grey Heron); lines 3–4: eggshell swabs (Grey Heron); lines 5–6: pin feathers (Purple Heron); lines 7–8: contour feathers (Great Egret); 9: negative control; M: molecular marker.
FIGURE 6 in DNA extracted from museum specimens of the 19 century provides a taxonomic resolution on the identity of the characid fish Psalidodon jequitinhonhae (Ostariophysi: Characiformes)
FIGURE 6 | Psalidodon jequitinhonhae. Two live specimens from Fanado River, tributary of Araçuaí River, Barragem das Almas, Minas Novas Municipality, Minas Gerais State, Brazil, Jequitinhonha River basin, 17°14'16.1"S 42°35'25.9"W. MZUEL 16425, not measured. Photo: José L. O. Birindelli.
FIGURE 5 in DNA extracted from museum specimens of the 19 century provides a taxonomic resolution on the identity of the characid fish Psalidodon jequitinhonhae (Ostariophysi: Characiformes)
FIGURE 5 | Psalidodon jequitinhonhae, LBP 8311, 55.9 mm SL. To the left: lateral view of maxillary, premaxillary and dentary teeth. To the right: medial view of premaxillary and dentary teeth.
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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)
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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.