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2,880 results for “variant”
A pharmacological chaperone stabilizer rescues the expression of the vast majority of pathogenic variants in a G protein-coupled receptor
Open the record for dataset details and reuse information.
Supplemental Material - An IL-6 promoter variant (-174 G/C) augments IL-6 production and alters skeletal muscle transcription in response to exercise in mice.
<p>Supplemental Material for article: "An IL-6 promoter variant (-174 G/C) augments IL-6 production and alters skeletal muscle transcription in response to exercise in mice."</p>
SARS-CoV-2 exposure in Malawian blood donors: an analysis of seroprevalence and variant dynamics between January 2020 and July 2021
<p>Results of population-based age stratified seroepidemiological investigation in Malawi.</p>
16S rDNA sequence data of research--Different periods of high-fat diet during peri-pregnancy cause variant offspring gut microbiota
<p> These are the 16S rRNA gene sequencing data based on the Illumina HiSeq2500 platform. Group a, b, c, d stand for group CD-CD, CD-HFD, HFD-CD, HFD-HFD separately. Each mouse of one group had two samples such as a1_1 and a1_2.</p>
Molecular modelling of novel ADCY3 variant predicts a molecular target for tackling obesity
<p>The present study aimed to identify <em>ADCY3</em> genetic variants in severely obese young patients of Greek-Cypriot origin by genomic sequencing. Total genomic DNA samples were isolated from peripheral whole blood using the Gentra Puregene Blood kit (Qiagen GmbH). DNA sequencing was performed with 100 ng genomic DNA, which was amplified using primers designed by Primer3 software ver. 0.4.0 (http://frodo.wi.mit.edu/). PCR mixtures were prepared using the Taq DNA Polymerase Kit (Qiagen GmbH); they had a final volume of 20 μl and contained 2 μl PCR buffer (10X), 2 μl Q Solution (5X), 2 μl dNTPs (2mM), 0.3 μl of each primer (10μM), 0.2 μl Taq polymerase (5U/μl) and 100 ng genomic DNA. Amplification was performed with an initial denaturing temperature at 95˚C for 5 min, followed by 30 cycles of denaturation (95˚C, 45 sec), annealing (57˚C, 60 sec) and extension (72˚C, 45 sec), with a final extension at 72˚C for 5 min. The <em>ADCY3</em> gene primers covered all exons. The PCR products were analysed on an Applied Biosystems 3130xl Genetic Analyzer and the results were analysed using Sequencing Analysis R 5.3 software (Applied Biosystems; Thermo Fisher Scientific, Inc.). The results revealed a total of five variants in patients, four of which were previously reported. A novel variant was identified in two patients (6%). The novel variant involves a heterozygous c.349T>A change in exon 1 of the gene locus, leading to a missense p.Leu117Met substitution.</p>
Impact of New Variants on SARS-CoV-2 Infectivity and Neutralization: A Molecular Assessment of the Alterations in the Spike-Host Protein Interactions
<p>MD simulation trajectories and structural models from the work which first appeared on bioRxiv (https://doi.org/10.1101/2021.01.10.426143), later ssrn (<a href="https://dx.doi.org/10.2139/ssrn.3907841">http://dx.doi.org/10.2139/ssrn.3907841</a>), and finally accepted for publication by Iscience.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run1_WT_RBD_ACE2.zip">Run1_WT_RBD_ACE2.zip</a></p> <p>Description: A compressed (zipped) folder contains three independent MD trajectories of WT RBD-ACE2 complex.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run2_N501Y_RBD_ACE2.zip">Run2_N501Y_RBD_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of Alpha RBD-ACE2 complex.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run3_Beta_RBD_ACE2.zip">Run3_Beta_RBD_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of Beta RBD-ACE2 complex.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run4_Delta_RBD_ACE2.zip">Run4_Delta_RBD_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of Delta RBD-ACE2 complex</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run5_UK2_E484K_N501Y_ACE2.zip">Run5_UK2_E484K_N501Y_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of UK2 RBD-ACE2 complex</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Structural_model_PDBs.zip">Structural_model_PDBs.zip</a></p> <p>Description: A compressed folder contains eight pdb files of those structural models plotted in Figs 1, 3, 5, 6, 7 and S1.</p>
eQTL Catalogue mapping from unique variant ids to rsIDs
<p>eQTL Catalogue mapping from unique variant ids to rsIDs</p>
Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants
<p>Scripts and metadata used in the analysis of the manuscript, <em>Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants.</em></p>
The 'dark matter' of protein variants carries a distinct DNA signature and predicts damaging variant effects
<p>Data generated for the manuscript "The 'dark matter' of protein variants carries a distinct DNA signature and predicts damaging variant effects".</p> <p> </p> <p>Please consult the README file for detailed description of data files included in this dataset.</p>
Dataset for human PDI wild-type and variants labeled at positions 57/401, 88/401, 57/467, and 88/467 with Atto 550/647N
<p>PTU files (time-correlated single-photon counting data) of freely diffusing human oxidized and reduced PDI wild-type and variants labeled at positions 57/401, 88/401, 57/467, and 88/467 with Atto 550/647N. </p> <p> </p> <p> </p>
ENDOG_NGS data related to article "Biallelic variants in ENDOG associated with mitochondrial myopathy and multiple mtDNA deletions" submitted to Cells
<p>vcf file of the targeted NGS; csv of the top 50 rare variants from WES prioritized by eVAI software; csv of WES rare variants prioritized by eVAI software using patient's phenotype information.</p>
Raw Data - Design and characterization of mutated variants of the oncotoxic parvoviral protein NS1
<p>Raw data of the Manuscript ''Design and characterization of mutated variants of the oncotoxic parvoviral protein NS1''</p> <p> </p>
Supplementary Information of Amplicon-based nanopore sequencing of patients with COVID-19 omicron (B.1.1.529) variant from India
<p><strong>We report sequencing of omicron variants from SARS-CoV-2 in 75 patients, using Nanopore long-read sequencing chemistry. We highlight the nature of mutations in spike glycoprotein that are unique and common to other populations.</strong></p> <p> </p>
Data from: Population genomic evidence of selection on structural variants in a natural hybrid zone
<p><span>Structural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long-read (Oxford nanopore) whole-genome sequencing and a hybrid zone between two </span><em>Lycaeides</em> butterfly taxa (<em>L. melissa</em> and Jackson Hole <em>Lycaeides</em>) to comprehensively evaluate genome-wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry-informative SVs exhibiting genomic clines that deviated from null expectations based on genome-average ancestry. Overall, hybrids exhibited a directional shift towards Jackson Hole <em>Lycaeides</em> ancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average than SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess ancestry from Jackson Hole <em>Lycaeides</em>. Excess Jackson Hole <em>Lycaeides</em> ancestry in hybrids was also especially pronounced for Z-linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might disproportionately affect hybrid fitness and thus contribute to reproductive isolation.</p>
Patch-clamp dataset (SyncroPatch384PE) for control variants used in a calibrated functional patch clamp assay to enhance clinical variant interpretation in KCNH2-related long QT syndrome
<p><span>Modern sequencing technologies have revolutionised our detection of gene variants. However, in most genes, including <em>KCNH2</em>, the majority of missense variants are currently classified as variants of uncertain significance (VUS). The aim of this study </span><span class="normaltextrun"><span>was to investigate the utility of an automated patch-clamp assay for aiding clinical variant classification in the <em>KCNH2 </em>gene. </span></span><span>The assay was designed according to recommendations proposed by the ClinGen Sequence Variant Interpretation Working Group. Thirty-one variants (17 pathogenic/likely pathogenic, 14 benign/likely benign) were classified internally as variant controls. They were heterozygously expressed in Flp-In HEK293 cells for assessing the effects of variant on current density and channel gating in order to determine the sensitive and specificity of the assay. All 17 pathogenic variant controls had reduced current density and 13/14 benign variant controls had normal current density, which enabled determination of normal and abnormal ranges for applying moderate or supporting evidence strength for VUS reclassification. Inclusion of <em>KCNH2</em> functional assay evidence enabled us to reclassify 6 out of 44 VUS as likely pathogenic. The high-throughput patch clamp assay can provide moderate strength evidence for clinical interpretation of clinical <em>KCNH2</em> variants and </span><span>demonstrates the value of developing automated patch clamp assays for functional characterisation of ion channel gene variants.</span></p>
DATASET - Vaccination and Variants: retrospective model for the evoultion of Covid-19 in Italy
<p>DATASET of <a href="https://medrxiv.org/cgi/content/short/2022.02.27.22271593v1">https://medrxiv.org/cgi/content/short/2022.02.27.22271593v1</a></p>
Comparison of missing data handling methods for variant pathogenicity predictors
<p>This upload contains result files from executing all experiments described in the manuscript.</p>
PRJNA578233 raw variants
<p>Sequencing reads were aligned to the Amel_HAv3.1 reference genome using BWA-MEM v0.7.17. Reads were sorted with SAMtools v1.9 and duplicates marked (MarkDuplicates) with GATK v4.0.11.0. Variants for each sample were called using GATK’s HaplotypeCaller with the following non-default parameters --ERC GVCF, --sample-ploidy 1 and -A AlleleFraction. Joint variant calling was performed across all samples collated for AmelHap using GATK’s GenomicDBImport and GenotypeGVCFs with --sample-ploidy 1 and a window size of 10 Mb. This dataset comprises the raw variant calls only for samples belonging to project accession: <a href="https://www.ebi.ac.uk/ena/browser/view/PRJNA578233">PRJNA578233</a>.</p>
Spatially variant immune infiltration scoring in human cancer tissues
<p>IMC raw dataset for cohort 1 and cohort 2 for the paper: "Spatially variant immune infiltration scoring in human cancer tissues"</p>
Twitter Conversations about the COVID-19 Omicron Variant: A Large Scale Dataset of more than 500,000 Tweets
<p><strong>Please cite the following paper when using this dataset:</strong></p> <p>N. Thakur and C.Y. Han, “An Exploratory Study of Tweets about the SARS-CoV-2 Omicron Variant: Insights from Sentiment Analysis, Language Interpretation, Source Tracking, Type Classification, and Embedded URL Detection,” Journal of COVID, 2022, Volume 5, Issue 3, pp. 1026-1049</p> <p><strong>Abstract</strong></p> <p>This open-access dataset is one of the salient contributions of the above-mentioned paper. It presents a total of <strong>522,886</strong> Tweet IDs of the same number of <strong>Tweets about the SARS-CoV-2 Omicron Variant</strong> posted on Twitter since the first detected case of this variant on November 24, 2021. The dataset is compliant with the privacy policy, developer agreement, and guidelines for content redistribution of Twitter, as well as with the FAIR principles (Findability, Accessibility, Interoperability, and Reusability) principles for scientific data management.</p> <p><strong>Data Description</strong></p> <p>The Tweet IDs are presented in 7 different .txt files based on the timelines of the associated tweets. The data collection followed a keyword-based approach and tweets comprising the "omicron" keyword were filtered, collected, and added to this dataset. The following is the description of these dataset files.</p> <ul> <li>Filename: TweetIDs_November.txt (No. of Tweet IDs: 16471, Date Range of the Tweet IDs: November 24, 2021 to November 30, 2021)</li> <li>Filename: TweetIDs_December.txt (No. of Tweet IDs: 99288, Date Range of the Tweet IDs: December 1, 2021 to December 31, 2021)</li> <li>Filename: TweetIDs_January.txt (No. of Tweet IDs: 92860, Date Range of the Tweet IDs: January 1, 2022 to January 31, 2022)</li> <li>Filename: TweetIDs_February.txt (No. of Tweet IDs: 89080, Date Range of the Tweet IDs: February 1, 2022 to February 28, 2022)</li> <li>Filename: TweetIDs_March.txt (No. of Tweet IDs: 97844, Date Range of the Tweet IDs: March 1, 2022 to March 31, 2022)</li> <li>Filename: TweetIDs_April.txt (No. of Tweet IDs: 91587, Date Range of the Tweet IDs: April 1, 2022 to April 20, 2022)</li> <li>Filename: TweetIDs_May.txt (No. of Tweet IDs: 35756, Date Range of the Tweet IDs: May 1, 2022 to May 12, 2022)</li> </ul> <p>In the above table, the last date for May is May 12 as it was the most recent date at the time of data collection and dataset upload. The dataset would be updated soon to incorporate more recent tweets.</p> <p>The dataset contains only Tweet IDs in compliance with the terms and conditions mentioned in the privacy policy, developer agreement, and guidelines for content redistribution of Twitter. The Tweet IDs need to be hydrated to be used. For hydrating this dataset the Hydrator application (<a href="https://github.com/DocNow/hydrator/releases">link to download</a> and a <a href="https://towardsdatascience.com/learn-how-to-easily-hydrate-tweets-a0f393ed340e#:~:text=Hydrating%20Tweets">step-by-step tutorial</a> on how to use Hydrator) may be used.</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.