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54 results for “NGS DATA”
Data from: Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies
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Data from: Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: validating a reverse workflow for specimen processing
Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an NGS barcoding pipeline that allows for cost-effective high throughput generation of short specimen-specific barcodes (313 bp of COI; lab cost <$0.50 per specimen) through Next Generation Sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3290 of 4032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88-90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases, and yields precise abundance information.
Data from: NGS library preparation may generate artifactual integration sites of AAV vectors
[No abstract entered]
Set of NGS raw data
<p>16SrDNA NGS raw data from Reunion island (Indian Ocean)</p> <p>- (i) from plastics (plastisphere) collected in sand or seawater on West or East coast,</p> <p>- (ii) sédiment or seawater sampled on West or East coast,</p>
Expanding NGS Data with Optical Genome Mapping (OGM)
ClinicalTrials.gov study NCT06851377. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Data from: NGS library preparation may generate artifactual integration sites of AAV vectors
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Data from: Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: validating a reverse workflow for specimen processing
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Data from: Evaluating NGS methods for routine monitoring of wild bees: metabarcoding, mitogenomics or NGS barcoding
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Very Long Baseline Interferometry (VLBI) National Geodetic Survey (NGS) card data from NASA CDDIS
Very Long Baseline Interferometry (VLBI) ASCII files in the NGS card format. Very Long Baseline Interferometry (VLBI) auxiliary ASCII files provided by the International VLBI Service for Geodesy and Astrometry (IVS) include schedules, notes, and session log files.
The histone acetyltransferase Mst2 prevents epigenetic silencing via specific acetylation of the ubiquitin ligase Brl1 [NGS data]
GEO Series GSE93432. Schizosaccharomyces pombe. 10 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Sex blind: bridging the gap between drug exposure and sex-related gene expression in Danio rerio using next-generation sequencing (NGS) data and a literature review to find the missing links in pharma
GEO Series GSE234104. Danio rerio. 6 samples. Type: Expression profiling by high throughput sequencing.
Raw ILLUMINA NGS data from study on Mouse virulence of European type III and type II x III-recombinant natural clones of Toxoplasma gondii is not always linked to the ROP18 and ROP5 genotype
<ul> <li>Whole genome sequences of naturally recombinant European type III and type II x III clones were analyzed</li> <li>While two of the type II x III recombinants showed an intermediate mouse virulence, a type III clone was highly virulent </li> <li>Of the three highly virulent clones, only two showed a virulent <em>ROP18</em>-<em>ROP5</em> allele combination</li> <li>The mouse virulent type III clone without virulent <em>ROP18</em>-<em>ROP5</em> allele combination showed the highest level of ROP5 mRNA expression</li> <li>Two genetically similar clones showed apparent differences in virulence and corresponding IL-12 mRNA expression in infected macrophages </li> </ul>
Childhood Cancer Data Initiative (CCDI): OncoKids - NGS Panel for Pediatric Malignancies
This study aimed to systematically collect clinical, registry and genomic data on pediatric cancer patients, and to contribute to the CCDI Pediatric Data Ecosystem. Clinical, treatment and outcome data on 1,039 pediatric cancer patients whose molecular profile was characterized on OncoKids gene panel at Children's Hospital Los Angeles was abstracted and harmonized for submission to the NCI's Cancer Data Service. The OncoKids panel was designed to detect DNA mutations and amplification in almost 200 oncogenes and tumor suppressor genes, a limited number of pharmacogenomic targets and 1,700 disease-associated gene fusions at the RNA level. The panel encompasses the vast majority of FDA's relevant pediatric molecular target list, as well as additional genes associated with ultra-rare pediatric tumors. The final data elements included DNA/RNA sequence data, OncoKids test results, clinical data on demographics, diagnosis, comorbidity and adverse events and treatment data.
Genome-wide bisulfite sequencing (Xmal-RRBS) of 50 breast cancer samples for jointly using with NGS and chromosomal microarray data
GEO Series GSE190126. Homo sapiens. 50 samples. Type: Methylation profiling by high throughput sequencing.
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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.