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2,880 results for “variant”
MIGNEX Survey Dataset (open-access variant)
<p>This is the anonymized variant of the MIGNEX Survey dataset. Please see MIGNEX Handbook Chapter 10 on how the anonymization process has affected the data.</p>
Training data for "Identification of allelic variants in SARS-CoV-2 from deep sequencing reads"
<p>Effectively monitoring global infectious disease crises, such as the COVID-19 pandemic, requires capacity to generate and analyze large volumes of sequencing data in near real time. These data have proven essential for monitoring the emergence and spread of new variants, and for understanding the evolutionary dynamics of the virus.</p> <p>Two sequencing platforms in combination with several established library preparation strategies are predominantly used to generate SARS-CoV-2 sequence data. However, data alone do not equal knowledge: they need to be analyzed. The Galaxy community developed analysis workflows to support the <strong>identification of allelic variants (AVs) in SARS-CoV-2 from deep sequencing reads</strong>.</p> <p>These workflows allow one to identify AVs and lineages in SARS-CoV-2 genomes with variant allele frequencies ranging from 5% to 100% (i.e., they detect variants with intermediate frequencies as well.</p> <p>In this tutorial we will see how to run these workflows for the different types of input data:</p> <ul> <li>Single end data derived from Illumina-based RNAseq experiments</li> <li>Paired end data derived from Illumina-based RNAseq experiments</li> <li>Paired-end data generated with Illumina-based Ampliconic (ARTIC) protocols</li> <li>ONT fastq files generated with Oxford nanopore (ONT)-based Ampliconic (ARTIC) protocols</li> </ul> <p>To illustrate the tutorial, we took some example datasets (paired-end data generated with Illumina-based Ampliconic (ARTIC) protocols) from COG-UK, the COVID-19 Genomics UK Consortium.</p>
Assembly of wild type and mutant variants of Enterohemorrhagic type IVa pili
<p>To analyse pilus assembly, bacteria of <em>E. coli</em> strain BW25113 F’<em>lacI</em><sup>Q</sup> were transformed with plasmid pMS41 encoding the EHEC pilus assembly genes and pCHAP8565 or its mutant derivatives encoding PpdD variants (Luna Rico et al. 2019). Bacteria were cultured for 48-72 hours on M9 minimal agar plates (Miller 1972) containing carbenicillin (100 mg.mL-1) and chloramphenicol (25 mg.mL-1). Bacteria were harvested and resuspended in LB medium at OD<sub>600nm</sub> of 1. The suspension was vortexed vigorously for 1 min to detach pili from bacteria. Bacteria were pelleted by 5-min centrifugation at 16000 g at 4°C and resuspended in SDS sample buffer at a concentration of 10 OD<sub>600nm</sub> per 1 mL. The supernatant containing pili was subjected to another round of centrifugation for 10 min. Pili were precipitated with 10% tri-chloroacetic acid on ice for 30 min and pelleted by a 30-min centrifugation at 16000g at 4°C. Pili pellets were washed twice with ice-cold acetone, air-dried and resuspended in SDS-sample buffer at a concentration equivalent to that of the bacteria. The equivalent volumes (5 ul) of each fraction were analysed by denaturing SDS polyacrylamide gel electrophoresis (SDS-PAGE) on 10% polyacrylamide Tris-Tricine gels (Schägger and Von Jagow 1987). Proteins were transferred on nitrocellulose by Western blot and probed with anti-PpdD antibodies and secondary anti-rabbit antibodies coupled to HRP as described (Luna Rico et al. 2019). The fluorescent signal was recorded with a Typhoon FLA-9000 scanner (GE).</p>
Molecular Dynamics of SARS-CoV-2 Delta Variant Receptor Binding Domain in Complex with ACE2 Receptor
<p>Molecular dynamics simulation for 10 ns at 37 C degrees of SARS-CoV-2 delta variant. Performed with NAMD and visualized/analyzed in ChimeraX software using Frontera supercomputer from Texas Advanced Computing Center. By Victor Padilla-Sanchez, PhD.</p> <p>https://www.youtube.com/watch?v=8N_MjWwxbMQ</p>
Assessing reproduciblity of Inherited Variants Detected with Short-read Whole Genome Sequencing
<p>This dataset is part of the following study:</p> <p><a href="https://www.fda.gov/science-research/bioinformatics-tools/microarraysequencing-quality-control-maqcseqc">https://www.fda.gov/science-research/bioinformatics-tools/microarraysequencing-quality-control-maqcseqc</a></p> <p>The raw sequencing data can be downloaded from SRA:</p> <p><a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA723125">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA723125</a></p> <p>and NODE:</p> <p><a href="https://www.biosino.org/node/project/detail/OEP0018966">https://www.biosino.org/node/project/detail/OEP0018966</a></p>
Source data for Neutralization of SARS-CoV-2 variants by convalescent and BNT162b2 vaccinated serum
<p>This dataset contains the source data used in the publication: "Neutralization of SARS-CoV-2 variants by convalescent and BNT162b2 vaccinated serum" published in Nature communications on August 26, 2021 (10.1038/s41467-021-25479-6).</p>
Simulated wastewater sequencing data for benchmarking SARS-CoV-2 variant abundance estimation
<p>To evaluate the accuracy of variant abundance predictions from wastewater sequencing, we built a collection of benchmarking datasets that resemble real wastewater samples. For each variant (B.1.1.7, B.1.351, B.1.427, B.1.429, P.1) we created a series of 33 benchmarks by simulating sequencing reads from a variant genome, as well as a collection of background (non-variant of concern/interest) sequences, such that the variant abundance ranges from 0.05% to 100%. Analogously, we created a second series of benchmarks, simulating reads only from the Spike gene of each SARS-CoV-2 genome. We refer to the first set of benchmarks as "whole genome" (WG) and to the second set of benchmarks as "S-only". We repeated these simulations at different sequencing depths: 100x and 1000x coverage for the whole genome benchmarks, and 100x, 1000x, and 10,000x coverage for the S-only benchmarks.</p>
Congenital disorder of glycosylation caused by starting site-specific variant in syntaxin-5
<p>The SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein syntaxin-5 (Stx5) is essential for Golgi transport. In humans, the <em>STX5</em> mRNA encodes two protein isoforms, Stx5 Long (Stx5L) from the first starting methionine and Stx5 Short (Stx5S) from an alternative starting methionine at position 55. In this study, we identified a novel human disorder caused by a single missense substitution in the second starting methionine (p.M55V), resulting in complete loss of the short isoform. Patients suffer from an early fatal multisystem disease, including severe liver disease, skeletal abnormalities and abnormal glycosylation. Primary human dermal fibroblasts isolated from these patients showed defective glycosylation, altered Golgi morphology as measured by electron microscopy and mislocalization of glycosyltransferases. Measurements of anterograde trafficking, based on biotin-synchronizable forms of Stx5 (the RUSH system), and of cognate binding SNAREs, based on Förster resonance energy transfer (FRET), revealed that the short isoform of Stx5 is essential for intra-Golgi transport. This is the first time a mutation in an alternative starting codon is linked to human disease, demonstrating that the site of translation initiation is an important new layer of regulating protein trafficking.</p>
dataset relared to article "Childhood‑onset dystonia‑causing KMT2B variants result in a distinctive genomic hypermethylation profile"
<p>Sanger sequences (.abi files) of all patients of Fondazione Besta cohort.</p>
Dataset of EPR-monitored-redox potentiometries performed with distinct CrFdx isoforms and variants
<p>The zip-folder contains the raw EPR data and data necessary for construction of the Nernst fits that appear in:</p> <p>Melanie Heghmanns, Alexander Günzel, Dörte Brandis, Yury Kutin, Vera Engelbrecht, Martin Winkler, Thomas Happe, Müge Kasanmascheff, "Fine-tuning of FeS Proteins Monitored via Pulsed EPR Redox Potentiometry at Q-band", Biophysical Reports, 2021, https://doi.org/10.1016/j.bpr.2021.100016.</p> <p>A brief explanation of the files and samples can be found in “Readme.docx”. <br> The relevant data obtained are compiled in “Summary_data.xlsx”. <br> Other experimental details can be found in the paper.</p>
Transcriptome analysis of T47D cells and H2A.J-KO derivatives for the paper entitled: The histone variant H2A.J is enriched in luminal epithelial gland cells
<p>H2A.J is a poorly studied mammalian-specific variant of histone H2A. We used immunohistochemistry to study its localization in various human and mouse tissues. H2A.J showed cell-type specific expression with a striking enrichment in luminal epithelial cells of multiple glands including those of breast, prostate, pancreas, thyroid, stomach, and salivary glands. H2A.J was also highly expressed in many carcinoma cell lines and in particular, those derived from luminal breast and prostate cancer. H2A.J thus appears to be a novel marker for luminal epithelial cancers. Knocking-out the H2AFJ gene in T47D luminal breast cancer cells reduced the expression of several estrogen-responsive genes which may explain its putative tumorigenic role in luminal-B breast cancer.</p>
V374A KCND3 pathogenic variant associated with paroxysmal ataxia exacerbations
<p><b>Objective</b></p> <p>Ataxia channelopathies share common features such as slow motor progression and variable degrees of cognitive dysfunction. Mutations in <i>KCND3, </i>encoding the K<sup>+</sup> channel, Kv4.3, are associated with spinocerebellar ataxia 19 (SCA19), allelic with spinocerebellar ataxia 22 (SCA22). Mutations in <i>KCNC3</i>, encoding another K<sup>+</sup> channel, Kv3.3, cause spinocerebellar ataxia 13 (SCA13). First, a comprehensive phenotype assessment was carried out in a family with autosomal dominant ataxia harboring two genetic variants in <i>KCNC3 </i>and <i>KCND3</i>. In order to evaluate the physiological impact of these variants on channel currents, <i>in vitro</i> studies were performed.</p> <p><b>Methods</b></p> <p>Clinical and psychometric evaluations, neuroimaging, and genotyping of a family (mother and son) affected by ataxia were carried out. Heterozygous and homozygous Kv3.3 A671V and<a name="_Hlk33945077">Kv4.3 V374A </a>variants were evaluated in <i>Xenopus laevis</i> oocytes using two-electrode voltage-clamp. The influence of Kv4 conductance on neuronal activity was investigated computationally using a Purkinje neuron model.</p> <p><b>Results</b></p> <p>The main clinical findings were consistent with adult-onset ataxia with cognitive dysfunction, and acetazolamide (ACZ)-responsive paroxysmal motor exacerbations in the index case. Despite cognitive deficits, FDG-PET displayed hypometabolism mainly in the severely atrophic cerebellum. Genetic analyses revealed the new variant <a name="_Hlk35066877">c.1121T>C (V374A), in <i>KCND3</i> and c.2012T>C (A671V) in <i>KCNC3</i></a>. <i>In vitro </i>electrophysiology experiments on <i>Xenopus</i> oocytes demonstrated that the V374A mutant was non-functional when expressed on its own. Upon equal co-expression of WT and V374A channel subunits, Kv4.3 currents were significantly reduced in a dominant negative manner, without alterations of the gating properties of the channel. In contrast, Kv3.3 A671V, when expressed alone, exhibited moderately reduced currents compared to WT, with no effects on channel activation or inactivation. Immunohistochemistry demonstrated adequate cell membrane translocation of the Kv4.3 V374A variant, thus suggesting an impairment of channel function, rather than of expression. Computational modeling predicted an increased Purkinje neuron firing frequency upon reduced Kv4.3 conductance.</p> <p><b>Conclusions</b> Our findings suggest that Kv4.3 V374A, is likely pathogenic and associated with paroxysmal ataxia exacerbations, a new trait for SCA19/22. The present FDG PET findings contrast with a previous study demonstrating widespread brain hypometabolism in SCA19/22.</p>
From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel
<p>In this dataset we provide the 1000 Genomes Project's samples processed in our manuscript:</p> <p>Cortes-Figueiredo, F.; Carvalho, F.S.; Fonseca, A.C.; Paul, F.; Ferro, J.M.; Schönherr, S.; Weissensteiner, H.; Morais, V.A. From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel. <em>Int. J. Mol. Sci</em>. <strong>2021</strong>, <em>22</em>, 12031. <a href="https://doi.org/10.3390/ijms222112031">https://doi.org/10.3390/ijms222112031</a><em>.</em></p> <p><strong>Abstract</strong></p> <p>Despite a multitude of methods for the sample preparation, sequencing, and data analysis of mitochondrial DNA (mtDNA), the demand for innovation remains, particularly in comparison with nuclear DNA (nDNA) research. The Applied Biosystems™ Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific, USA) is an innovative library preparation kit suitable for degraded samples and low DNA input. However, its bioinformatic processing occurs in the enterprise Ion Torrent Suite™ Software (TSS), yielding BAM files aligned to an unorthodox version of the revised Cambridge Reference Sequence (rCRS), with a heteroplasmy threshold level of 10%. Here, we present an alternative customizable pipeline, the PrecisionCallerPipeline (PCP), for processing samples with the correct rCRS output after Ion Torrent sequencing with the Precision ID library kit. Using 18 samples (3 original samples and 15 mixtures) derived from the 1000 Genomes Project, we achieved overall improved performance metrics in comparison with the proprietary TSS, with optimal performance at a 2.5% heteroplasmy threshold. We further validated our findings with 50 samples from an ongoing independent cohort of stroke patients, with PCP finding 98.31% of TSS’s variants (TSS found 57.92% of PCP’s variants), with a significant correlation between the variant levels of variants found with both pipelines.</p> <p><br> Please refer to our the github page <a href="https://github.com/filcfig/PCP.git">filcfig/PCP</a>, for more details on running the PrecisionCalllerPipeline.</p>
AMTraC-19 (v7.9) Dataset: Persistence of the Omicron variant of SARS-CoV-2 in Australia
<p>The paper describing scenarios which generated this dataset:</p> <p>S. L. Chang, Q. D. Nguyen, A. Martiniuk, V. Sintchenko, T. C. Sorrell, M. Prokopenko, Persistence of the Omicron variant of SARS-CoV-2 in Australia: The impact of fluctuating social distancing, <em>PLOS Global Public Health</em>, 3(4): e0001427, 2023.</p> <p>The AMTraC-19 source code (v7.9) is released on Zenodo: https://zenodo.org/record/7325675</p>
Dataset and code for the variants of the traveling salesman problem with time windows using multifactorial evolutionary algorithm
<p>Dataset and code for the variants of the traveling salesman problem with time windows using multifactorial evolutionary algorithm</p>
Force-tuned Avidity of Spike Variant-ACE2 Interactions viewed on the Single-Molecule Level - MD simulations Dataset
<p>Models of SARS-CoV-2 virus spike protein bound to 1-3 of ACE2 receptors embedded in lipid nanodisks. Systems include all files in GROMACS format needed to reproduce simulations performed in the "Force-tuned Avidity of Spike Variant-ACE2 Interactions viewed on the Single-Molecule Level" article.</p> <p> </p> <table> <caption>Details</caption> <thead> <tr> <th scope="col">system</th> <th scope="col">box size (x-y-z) [nm]</th> <th scope="col">Number of atoms</th> </tr> </thead> <tbody> <tr> <td>Spike +<br> 1x ACE2, full length</td> <td>33.44834 28.96711 57.95573</td> <td>5,665,217</td> </tr> <tr> <td>Spike +<br> 1x ACE2, truncated</td> <td>28.05757 24.29856 46.74417</td> <td>3,203,907</td> </tr> <tr> <td>Spike +<br> 2x ACE2, truncated</td> <td>28.30864 21.23141 48.40873</td> <td>2,936,398</td> </tr> <tr> <td>Spike +<br> 3x ACE2, truncated</td> <td>28.32733 21.24544 48.30436</td> <td>2,936,588</td> </tr> </tbody> </table>
Detection of SARS-CoV-2 variants by genomic analysis of wastewater ampliconic samples (Galaxy Training Material)
<p>The tutorial aims to train how to run workflows to analyze lineages abundances in SAR-CoV-2 wastewater ampliconic samples. (https://training.galaxyproject.org/training-material/)</p>
Detection of SARS-CoV-2 variants by genomic analysis of wastewater metatranscriptomic samples (Galaxy Training Material)
<p>The tutorial aims to train how to run workflows to analyze lineages abundances in SAR-CoV-2 wastewater metatranscriptomic samples. (https://training.galaxyproject.org/training-material/)</p>
The associations of gene-gene interactions among the 6 variants in 3 genes related to inflammation and endothelial function with carotid stenosis were performed by the GMDR approach
<p><span>The associations of gene-gene interactions among the 6 variants in 3 genes related to inflammation and endothelial function with carotid stenosis were performed by the GMDR approach. The best model for carotid stenosis including <em>ITGA2</em> rs4865756 and <em>HABP2</em> rs7923349 scored 8/10 for cross-validation consistency and 10/10 for sign testing. </span></p>
IDSL.CSA spectra annotation table for unique CSA variants of ST001000 - against public MS/MS databases
<p>IDSL.CSA spectra annotation table for unique CSA variants of ST001000 - against public MS/MS databases</p>
ScienceDex guides
Understand access before you commit
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.