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143 results for “DNA extract”
Figure 3 from: Camacho AI, Dorda BA, Chillón BS, Rey I (2017) The collection of Bathynellacea specimens of MNCN (CSIC) Madrid: microscope slices and DNA extract. ZooKeys 678: 31-63. https://doi.org/10.3897/zookeys.678.11543
Figure 3 - Bathynellacea genera by families in the MNCN collections versus world.
Figure 13 from: Camacho AI, Dorda BA, Chillón BS, Rey I (2017) The collection of Bathynellacea specimens of MNCN (CSIC) Madrid: microscope slices and DNA extract. ZooKeys 678: 31-63. https://doi.org/10.3897/zookeys.678.11543
Figure 13 - Number of records of Bathynellacea from Europe by countries in the MNCN collections.
Figure 12 from: Camacho AI, Dorda BA, Chillón BS, Rey I (2017) The collection of Bathynellacea specimens of MNCN (CSIC) Madrid: microscope slices and DNA extract. ZooKeys 678: 31-63. https://doi.org/10.3897/zookeys.678.11543
Figure 12 - Number of records of Bathynellacea by continents in the MNCN collections.
Figure 10 from: Camacho AI, Dorda BA, Chillón BS, Rey I (2017) The collection of Bathynellacea specimens of MNCN (CSIC) Madrid: microscope slices and DNA extract. ZooKeys 678: 31-63. https://doi.org/10.3897/zookeys.678.11543
Figure 10 - Number of species of Bathynellacea by continents and families in the MNCN collections.
Figure 1 from: Camacho AI, Dorda BA, Chillón BS, Rey I (2017) The collection of Bathynellacea specimens of MNCN (CSIC) Madrid: microscope slices and DNA extract. ZooKeys 678: 31-63. https://doi.org/10.3897/zookeys.678.11543
Figure 1 - Familiy records in the MNCN collections.
Extracting Regulatory Chromatin Footprint from Cell-Free DNA
<p>Cell-free DNA (cfDNA) has emerged as a pivotal player in precision medicine, revolutionizing the diagnostic and therapeutic landscape. While its clinical applications have significantly increased in recent years, current cfDNA assays have limited ability to identify the active transcriptional programs that govern complex disease phenotypes and capture the heterogeneity of the disease. To address these limitations, we have developed a non-invasive platform to enrich and examine the active chromatin fragments (cfDNAac) in peripheral blood. The deconvolution of the cfDNAac signal from traditional nucleosomal chromatin fragments (cfDNAnuc) yields a catalog of features linking these circulating chromatin signals in blood to specific regulatory elements across the genome, including enhancers, promoters, and highly transcribed genes, mirroring the epigenetic data from the ENCODE project. Notably, these cfDNAac counts correlate strongly with RNA polymerase II activity and exhibit distinct expression patterns for known circadian genes. Additionally, cfDNAac signals across gene bodies and promoters show strong correlations with whole blood gene expression levels defined by GTEx. This study illustrates the utility of cfDNAac analysis for investigating epigenomics and gene expression, underscoring its potential for a wide range of clinical applications in precision medicine.</p>
Improved detection of DNA Schistosoma haematobium from eggs extracted by bead beating in urine
<p>Diagnosis of Schistosoma haematobium relies primarily on microscopical analysis of urine. The method is time consuming and<br> requires some expertise. Genus-specific real-time PCRs have been developed, but we still observed low sensitivity. In the present<br> study, in order to achieve a more sensitive DNA detection of eggs of S. haematobium in urine samples, we wanted to develop a<br> novel protocol of DNA extraction using mechanic disruption of eggs by bead beating as supplementary step. We tested<br> Schistosoma spp. internal transcribed spacer 2 real-time PCR after both methods with and without bead beating. First, we<br> preliminary assessed the DNA detection after bead beating using dilution of 2, 10, 50, and 90 eggs/10 mL, and the Ct value<br> analysis showed significant improved DNA detection per each point of egg concentration using the novel supplementary step.<br> Twenty microscopy positive and five microscopy negative urine samples were used to validate the procedure. All urines came<br> from imported cases and admitted at center for tropical medicine, and were examined by microscopy. PCR results after novel<br> method with bead beating showed 100% to be positive for S. haematobium, compared with 85% positive by our standard<br> extraction procedure. Results confirmed mechanic disruption of eggs by bead beating before DNA extraction to be highly<br> effective method for the detection of S. haematobium DNA in urine.</p>
Data from: Direct PCR meets high-throughput sequencing - metabarcoding of chironomid communities without DNA extraction
<p>Abstract</p> <p>Metabarcoding is a valuable tool for investigating insect community compositions. However, high-throughput applications, such as for biomonitoring, require cost-effective and user-friendly procedures. To investigate if the time-consuming and labour-intensive DNA isolation step can be omitted in metabarcoding, we studied the difference in detection rates and individual read abundance using standard DNA isolation versus direct PCR protocols. Metabarcoding with and without DNA isolation was performed on artificially created communities with known composition as well as on natural communities both of the dipteran family Chironomidae to compare detection rates, individual read abundances and presence-absence community composition. The data sets include read abundances of all artificial and natural community samples. Compositions of the samples per data set are described in the respective README files. ASVs/OTUs and their respective DNA sequences are given. R Scripts for bioinformatic processing (dada2 for ASVs, JAMP for OTUs) are provided.</p> <p>Methods</p> <p>Chironomidae were retrieved from artificial ponds of the Eußerthal Ecosystem Research Station (EERES) near Landau, Germany, in 2019 and 2020. Adult specimens were collected from passive emergence traps. Chironomid samples were stored in 70% ethanol and later dried at 60°C. Samples were then finely ground using a bead mill. PCR-grade water was added to each tissue sample and thoroughly vortexed. The tissue-water mixes were frozen at -20°C until further analysis. Artificial communities were created by pipetting tissue-water mixes of individual chironomids. Natural communities from eight ponds and five consecutive sampling dates were selected to assess the applicability of the dPCR approach compared to standard metabarcoding protocols on natural chironomid communities. Four of the artificial ponds were treated with the mosquito control agent <em>Bacillus thuringiensis israelensis</em> (Bti). Tissue-water mixes of artificial and natural communities were both directly applied to PCR and used for DNA isolation. Illumina sequencing was performed and raw data were bioinformatically prepared. For more details see "Direct PCR meets high-throughput sequencing - metabarcoding of chironomid communities without DNA extraction" (Röder & Schwenk 2023). Raw sequences are available through GenBank SRA archive (BioProject accession number PRJNA989176). </p>
Detection of Azole Resistance Inducing Mutations on DNA Extracted Directly From Serum or Plasma of Immunocompromised Patients With an Invasive Aspergillus Infection Azole Resistance PCR Optimalization
ClinicalTrials.gov study NCT06069505. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Evaluation of PCR Using DNA Extract From Slides and Filter Paper for the Detection of Tuberculosis and MDR-tuberculosis
ClinicalTrials.gov study NCT03137875. IPD Sharing: NO. Countries: 1. Publications: 0.
Testing of DNA Extracted From Tumor Tissue Biopsy Samples Using Therascreen KRAS RGQ PCR Kit
ClinicalTrials.gov study NCT05360225. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Clinical Study Testing DNA Extracted From Tumour Tissue Biopsy Samples, Using the Therascreen® KRAS RGQ PCR Kit
ClinicalTrials.gov study NCT05347797. IPD Sharing: NO. Countries: 1. Publications: 0.
Microfluidic Extraction of DNA for Identification of Unknown organisms in Microgravity Project
<p>Expanding human spaceflight beyond low-Earth orbit poses significant technological challenges. One of these challenges is environmental monitoring, specifically the ability to identify and respond to microbiological threats in real-time. Because returning samples to Earth for analysis is not practical from deep-space, in-flight environmental monitoring is an essential capability for missions away from low-Earth orbit. Microbial identification by direct sequencing is readily achieved by identifying species-specific differences in Deoxyribonucleic Acid (DNA) sequences. These analyses require the extraction and separation of DNA from cells, but current methods for DNA isolation typically require technologies incompatible with spaceflight.</p><p>In-flight environmental monitoring is an important technology for missions away from low-Earth orbit. An important aspect of environmental monitoring is the ability to identify and respond to microbiological threats. Automatable in situ monitoring technologies are essential when sample return is not practical. Microbial identification is readily achieved by identifying differences in DNA sequences, such as direct sequencing or hybridization of the DNA strands. These analyses require the extraction and separation of DNA from cells. However, current methods for DNA isolation typically require technologies incompatible with spaceflight.</p><p>We seek to develop a miniaturized MEDIUM device for the extraction of DNA from operationally relevant samples (i.e., potable water sources); the extracted DNA can then be used for microbial identification using one or more DNA-dependent molecular techniques, such as sequencing. Isolation of DNA for sequencing or other analyses typically requires technologies incompatible with spaceflight. For this reason we have carefully chosen digital microfluidics-based extraction cartridges due to their likely compatibility with microgravity. Unlike other DNA extraction methods that rely on gravitational forces, the microfluidics devices use electro-wetting to move liquids. This eliminates the requirement for pumps, centrifuges and other moving parts. The quality of the DNA extracted by the microfluidics-based platform and by conventional kit-based methods will be characterized for its suitability in next-generation sequencing applications.</p>
Effects of Paramylon Extracted from Euglena gracilis EOD-1 on lipid metabolism in the Ileum and Liver in Diet-Induced Obese Mice Analyzed by DNA Microarray.
GEO Series GSE181289. Mus musculus. 4 samples. Type: Expression profiling by array.
Genome-wide promoter DNA Methylation Profiling of Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Exposure to Ginkgo biloba Extract (GBE) in B6C3F1/N Mice [Methylation]
GEO Series GSE132577. Mus musculus. 15 samples. Type: Methylation profiling by genome tiling array.
Modifying DNA extraction protocol alters human brain copy number estimation
GEO Series GSE71470. Homo sapiens. 40 samples. Type: Genome variation profiling by array; SNP genotyping by SNP array.
Early life Lead exposure causes distinct gender specific changes in the DNA methylation profile of DNA extracted from dried blood spots
GEO Series GSE60598. Homo sapiens. 43 samples. Type: Methylation profiling by genome tiling array.
The effects from DNA extraction methods on the evaluation of microbial diversity associated with human colonic tissue
GEO Series GSE18420. human gut metagenome; Archaea; Bacteria. 12 samples. Type: Expression profiling by array.
Effect of DNA extraction method on brain DNA copy number estimation
GEO Series GSE71360. Homo sapiens. 25 samples. Type: Genome variation profiling by array.
Facilitating high throughput collections-based genomics: a comparison of DNA extraction and library build methods
<p>Dataset for submission: "Facilitating high throughput collections-based genomics: a comparison of DNA extraction and library build methods"</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.