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2,880 results for “variant”
Implementation of Genomic Variant Calling Using GATK4, SPARK, WDL, CROMWELL and DOCKER Over Simulated Ebola NGS Dataset.
<p>Ebola genome is manually mutated to contain non-structural variants - 10 SNPs, 10 INDELs, 05 TRANSLOCATIONs, 05 INSERSIONs and their reverse complements. Paired-end illumina RNASEQ reads are simulated in fastq format. </p>
Implementation of Genomic Variant Calling Using GATK4, SPARK, WDL, CROMWELL and DOCKER Over Simulated Ebola NGS Dataset.
<p>Ebola genome is manually mutated to contain structural variants. There are seven mutated ebola genomes each one for two large deletions, insertions, duplications, translocations, inversions, one complex variant1 (consecutive three mutations - insertion, duplication and deletion) and one complex variants2 (consecutive three mutations - deletion, duplication and deletion). All insertions are novel sequence insertion. Paired-end illumine RNASEQ reads are simulated in fastq format.</p>
Implementation of Genomic Variant Calling Using GATK4, SPARK, WDL, CROMWELL and DOCKER Over Simulated Ebola NGS Dataset.
<p>Ebola genome is manually mutated to contain structural variants. There are seven mutated ebola genomes each one for large deletion, insertion, duplication, translocation, inversion, complex variant1 (consecutive three mutations - insertion, duplication and deletion) and complex variants2 (consecutive three mutations - deletion, duplication and deletion). All insertions are novel sequence insertion. Paired-end illumine RNASEQ reads are simulated in fastq format.</p>
Raw diffraction data for [NiFeSe] hydrogenase G491S variant pressurized with O2 gas - dataset G491S-O2
<p>Diffraction data measured at ESRF beamline ID29 on October 2, 2017.</p> <p>Image files are uploaded as blocks of cbf files in gzip-compressed tar files.</p>
Raw diffraction data for [NiFeSe] hydrogenase G491A variant pressurized with O2 gas - dataset G491A-O2-HD
<p>Diffraction data measured at ESRF beamline ID30B on April 8, 2018.</p> <p>Image files are uploaded in blocks of gzip-compressed cbf files.</p>
Datasets for GTN tutorial on SARS-CoV-2 variant analysis
<p>A reference genome in FASTA format is provided for SARS-CoV-2, "Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome", having the accession ID of NC_045512.2.</p> <p>This file was obtained from NCBI within this Galaxy history: https://usegalaxy.org/u/dan/h/nc0455122-from-ncbi</p>
VariaNTS corpus: A spoken Dutch corpus containing talker and linguistic variability
<p>The VariaNTS (Variatie in Nederlandse Taal en Sprekers) corpus is a Dutch spoken corpus that was developed to maximize both linguistic and talker variability. It contains 1000 stimulus materials from 11 linguistic subcategories, recorded by 8 male and 8 female native speakers of standard Dutch. The corpus contains audio recordings, orthographic transcriptions, stimulus-specific details such as word frequencies, neighborhood densities and phonotactic probabilities, and talker details. The VariaNTS corpus aims to provide new materials to be used for broad assessment of speech perception and word recognition in Dutch clinical and academic settings. </p>
Amplicon sequence variants by sample table from Antarctic methane seeps
<p>Antarctica is estimated to contain as much as a quarter of earth's marine methane, however we have not discovered an active Antarctic methane seep limiting our understanding of the methane cycle. In 2011, an expansive (70m x 1m) microbial mat formed at 10m water depth in the Ross Sea, Antarctica and we carried out 16S rRNA gene analysis on samples collected one year and five years after the methane seep formed. The data set attached is the resulting Amplicon Sequence Variant table by sample that we used to track the community composition change during this time and in comparison to other sampling in the McMurdo sound region. </p>
Identification and characterization of novel splice variants of human farnesoid X receptor
<p>Dataset related to publication:</p> <blockquote> <p>Mustonen E-K, Lee SML, Nieß H, Schwab M, Pantsar T, Burk O: "Identification and characterization of novel splice variants of human farnesoid X receptor". <em>Archives of Biochemistry and Biophysics</em> <a href="https://doi.org/10.1016/j.abb.2021.108893">https://doi.org/10.1016/j.abb.2021.108893</a></p> </blockquote> <p> </p> <p>Including:</p> <p>I. Full-length raw-trajectories of the 1 microsecond Desmond simulations (-out.cms, trj)</p>
Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species
<p>Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. To date, our knowledge of genotypic variation and evolution has largely been acquired by means of single nucleotide polymorphism (SNPs) analyses. Until recently, the adaptive role of structural variants (SVs) and particularly that of CNVs has been overlooked in wild populations, partly due to their challenging identification. Here, we document the usefulness of Rapture, a derived reduced‐representation shotgun sequencing approach, to detect and investigate copy number variants (CNVs) alongside SNPs in American lobster (<i>Homarus americanus</i>) populations. We conducted a comparative study to examine the potential role of SNPs and CNVs in local adaptation by sequencing 1,141 lobsters from 21 sampling sites within the southern Gulf of St. Lawrence, which experiences the highest yearly thermal variance of the Canadian marine coastal waters. Our results demonstrated that CNVs account for higher genetic differentiation than SNP markers. Contrary to SNPs, for which no significant genetic–environment association was found, 48 CNV candidates were significantly associated with the annual variance of sea surface temperature, leading to the genetic clustering of sampling locations despite their geographic separation. Altogether, we provide a strong empirical case that CNVs putatively contribute to local adaptation in marine species and unveil stronger spatial signal of population structure than SNPs. Our study provides the means to study CNVs in nonmodel species and highlights the importance of considering structural variants alongside SNPs to enhance our understanding of ecological and evolutionary processes shaping adaptive population structure.</p>
Rare variant replaced Korea reference genome fasta
<p>The rare variants of Korea reference genome fasta were replaced with using 396 Korean vcf information</p>
CusVarDB: A tool for building customized sample-specific variant protein database from Next-generation sequencing datasets
<p>CusVarDB is a windows based tool for creating a variant protein database from Next-generation sequencing datasets. The program supports variant calling for Genome, RNA-Seq and exome datasets.</p> <p>This repository will provide the resultant variant peptides identified in our study and its corresponding information. The detailed information of the table is given below.</p> <p>Supplementary Table 1. This table contains the resultant variant peptides along with its wild-type peptides from BT474, MDMAB157, MFM223, and HCC38 datasets. Along with mutant peptides, this section also provides additional information such as peptide-spectrum match (PSM), Protein accession, cross-correlation value from the search (Xcorr), and retention time (RT).</p> <p>Supplementary Table 2. This table provides the complete details of the resultant peptides. Here the mutant and corresponding wild-type peptides are mentioned in different sheets. For a given mutant peptide its wild-type peptide and corresponding information can be mapped using the VLOOKUP function in Excel by keeping column A (Sl.No) as lookup parameter.</p> <p>Supplementary Table 3. This table briefs about the variants which are already reported in other cancers.</p>
Genetic variants beyond amyloid and tau associated cognitive decline: a cohort study
<p>Objective: To identify single nucleotide polymorphisms (SNPs) associated with cognitive decline independent of amyloid &[beta] (A&[beta]) and tau pathology in Alzheimer's disease (AD). Methods: Discovery and replication datasets consisting of 414 subjects (94 cognitively normal control [CN), 185 with mild cognitive impairment [MCI], and 135 AD) and 72 subjects (22 CN, 39 MCI, and 11 AD), respectively, were obtained from the Alzheimer's Disease Neuroimaging Initiative database. Genome-wide association analysis was conducted to identify SNPs associated with individual cognitive function (measured using the MMSE and ADAS-cog) while controlling for the level of A&[beta] and tau (measured as CSF p-tau/A&[beta]1-42). Gene ontology analysis was performed on SNP associated genes.</p> <p>Results: We identified one significant (rs55906536, &[beta]=-1.91,standard error 0.34, P =4.07×10<sup>-8</sup>) and four suggestive variants on chromosome 6, which were associated with poorer cognitive function. Congruent results were found in the replication data. A structural equation model showed that the identified SNP deteriorated cognitive function partially through cortical thinning of the brain in a region-specific manner. Furthermore, a bioinformatics analysis showed that the identified SNPs were associated with genes related to glutathione metabolism.</p> <p>Conclusions: In this study, we identified SNPs related to cognitive decline, in a manner which could not be explained by A&[beta] and tau levels. Our findings provide insight into the complexity of AD pathogenesis and support the growing literature on the role of glutathione in AD. This study suggests anti-oxidative agents may serve therapeutic for AD subjects with the identified SNPs.</p>
Querying variants. Boccaccio's Commedia
<p>6th Project Presentation</p>
A SLC1A3 variant associated with hemiplegic migraine and acetazolamide-responsive MRS changes
<p>Familial hemiplegic migraine (FHM) is a group of rare familial disorders caused, in most cases, by mutations in <em>CACNA1A</em> and <em>ATP1A2</em>.<sup><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357413/#R1">1</a></sup> Heterozygous mutations in solute carrier family 1 member 3 (<em>SLC1A3</em>), encoding glial glutamate transporter, are associated with episodic ataxia type 6 (EA6).<sup><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357413/#R2">2</a>,<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357413/#R3">–</a><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357413/#R5">5</a></sup> In addition to episodic ataxia (EA), alternating hemiplegia and hemiplegic migraine have been reported twice in patients with EA6.<sup><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357413/#R2">2</a>,<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357413/#R4">4</a></sup> Mutations in <em>SLC1A3</em> are very rare; screenings in cohorts of EA and alternating hemiplegia have yielded either negative results<sup><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357413/#R3">3</a>,<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357413/#R6">6</a>,<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357413/#R7">–</a><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357413/#R8">8</a></sup> or variants of unclear significance.<sup>e-1--e-3</sup> Herein, we characterize a patient featuring sporadic hemiplegic migraine (SHM) responsive to acetazolamide (ACZ) and mild cerebellar atrophy associated with a new variant in <em>SLC1A3.</em> We also report the utility of proton magnetic resonance spectroscopy (MRS) for this condition.</p>
Dataset for testing the calibration of the variant prediction methods
<p>Dataset used for testing the calibration of 6 methods for predicting the impact of single nucleotide variants in the publication: </p> <p><em>Benevenuta S, Capriotti E, Fariselli P</em>. (2021). Calibrating variant-scoring methods for clinical decision making. <strong>Bioinformatics</strong>. DOI: <a href="http://doi.org/10.1093/bioinformatics/btaa943">10.1093/bioinformatics/btaa943</a>.</p> <p>The file contains the following columns:</p> <ol> <li>CHROM: Chromosome number </li> <li>POS: Chromosome coordinate</li> <li>REF: Reference Allele </li> <li>ALT: Alternative Allele </li> <li>Coding: Coding Variants (Yes/No) </li> <li>Effect: Variant impact (Pathogenic/Benign) </li> <li>DANN: DANN output </li> <li>PhDSNP: PhD-SNPg output </li> <li>FATHMM: FATHMM output </li> <li>CADD: CADD output </li> <li>DeepSea: DeepSea output</li> <li>Eigen: Eigen output</li> </ol> <p> </p> <p> </p> <p> </p> <p> </p>
Annotated and classified variants from patients with MDS/AML detected in seven public datasets
<p>990 unique validated variants from patients with MDS/AML detected in seven public datasets (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA388411). Databases and web services were accessed for variant annotation and classification on September 7, 2020.</p>
Clinical variant databases
<p>Overview of all included and excluded databases for clinical variant annotation in cancer with the help of open-access databases. Databases and web links were last accessed on January 28, 2021.</p>
A specific IL6 polymorphic genotype modulates the risk of T. cruzi parasitemia while IL18, IL17A and IL1B variant profiles and HIV infection protect against cardiomyopathy in Chagas disease
<p><strong>Background:</strong> Chagas disease caused by Trypanosoma cruzi (T. cruzi) affects approximately six million individuals worldwide. Clinical manifestations are expected to occur due to the parasite persistence and host immune response. Herein we investigated potential associations between IL1B, IL6, IL17A or IL18 polymorphism profiles and cardiomyopathy or T. cruzi parasitemia, as well as the impact of HIV infection on cardiopathy.</p> <p><strong>Methods:</strong> 206 patients and 90 control individuals were analyzed. IL1B rs1143627 T>C, IL6 rs1800795 C>G, IL17A rs2275913 G>A, IL18 rs187238 C>G, and IL18 rs1946518 C>A SNVs were analyzed by real-time PCR and T. cruzi parasitemia by PCR.</p> <p><strong>Results: </strong>Our data revealed association between a cytokine gene polymorphism and parasitemia never previously reported. The IL6 rs1800795 CG genotype lowered the risk of positive parasitemia (OR=0.45, 95% CI 0.24–0.86, P=0.015). Original findings included associations between IL17A rs2275913 AA and IL18 s1946518 AA genotypes with decreased risk of developing cardiomyopathy (OR=0.27, 95% CI 0.07-0.97, P=0.044; and OR=0.35, 95% CI 0.14-0.87, P=0.023, respectively). IL18 rs1946518 AA and IL1B rs1143627 TC were associated with reduced risk for cardiomyopathy severity, including NYHA (New York Heart Association) class≥ 2 (OR=0.21, 95% CI 0.06-0.68, P=0.009; and OR=0.48, 95% CI 0.24-0.95, P=0.036, respectively) and LVEF (Left Ventricular Ejection Fraction) <45% for IL18 rs1946518 AA (OR=0.22, 95% CI 0.05-0.89, P=0.034). A novel, unexpected protective effect of HIV infection against development/progression of cardiomyopathy was identified, based on a lower risk of developing cardiopathy (OR=0.48, 95% CI 0.23‐0.96, P=0.039), NYHA class≥2 (OR=0.15, 95% CI 0.06‐0.39, P<0.001) and LVEF<45% (OR=0.03, 95% CI 0.00‐0.25, P=0.001). Digestive involvement was negatively associated with NYHA ≥2 and LVEF<45% (OR=0.20, 95% CI 0.09‐0.47, P<0.001; and OR=0.24, 95% CI 0.09-0.62, P=0.004, respectively).</p> <p><strong>Conclusions: </strong>Our data support a protective role of IL17A AA, IL18 AA and IL1B TC genotypes against development/progression of cardiomyopathy and a modulatory effect of the IL6 CG genotype on the risk of parasitemia in Chagas disease. Notably, HIV infection was shown to protect against development/progression of cardiopathy, potentially associated with a synergistic effect of HIV and HAART, attenuating a Th1-mediated response in the myocardium. This proposed hypothesis requires confirmation, however, in larger and more comprehensive future studies.</p>
Caméra 16 mm Bolex Auto-Ciné B variante 1
Ce contenu fait partie de l'*[Encyclopédie raisonnée des techniques du cinéma](http://encyclo-technes.org/fr)*, publiée par le Partenariat international de recherche sur les techniques et technologies du cinéma TECHNÈS. This content is part of the *[Encyclopedia of Film Techniques and Technologies](http://encyclo-technes.org/en)*, published by the International Research Partnership on Cinema Technology, TECHNÈS. ___ **Institution de conservation/holding institution: **Université Laval **Cote/accessing number: **Collection Lemai, L.sc.1178 **Numérisation et postproduction/digitizing and postproduction: **Bérubé, Patricia; Cloutier, Michael; Deslongchamps, Maxime; Raginel, Joachim **Dates de numérisation/digitizing dates: **2017-07-10/2017-07-14 **Droits/rights: **© TECHNÈS, 2017. Certains droits réservés/some rights reserved. **Identifiant/identifier: **[ark:/17444/902894/2214](http://encyclo-technes.org/fr/base/ark:/17444/902894/2214) Source: Objaverse 1.0 / Sketchfab
ScienceDex guides
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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.