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2,880 results for “variant”
De novo assemblies for the manuscrip "Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres"
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Stratified analyses refine association between TLR7 rare variants and severe COVID-19 - Datasets
<p>This dataset comprises single variant summary statistics (MAF>0.01%) and the results of the burden analyses for the publication <em>Stratified analyses refine association between TLR7 rare variants and severe COVID-19 </em>by Boos et al. 2024 in HGG Advances.</p> <p>Please refer to the respective README-Files for a description of the file contents.</p>
Molecular models of A501X variants of penicillin-binding protein PBP2
<p>Each archive comprices a set of PDB and PSF files for PBP2 and its A501V, A501P and A501R variants.</p> <p><a href="../api/records/11660179/draft/files/QMMM_MD_models.7z/content" target="_blank" rel="noopener">QMMM_MD_models.7z</a> –QMMM_MD_models.7z full-atom models for molecular dynamic simulations with periodic boundary conditions including QM/MM MD.</p> <p>MD_clusters.7z – representative frames from classical MD trajectories. Of particular importance is conformation of β<sub>3</sub>-β<sub>4</sub> loop (residues 498-514).</p> <p> </p>
Kufor-Rakeb Syndrome-Associated Psychosis: A Novel Loss-of-Function ATP13A2 Variant and Response to Antipsychotic Therapy
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Dataset of skin pigmentation related variants and interaction effects on serum vitamin D
<p>This dataset contains all SNPs-gene and phenotype analyzed in article <span><span><span>entitled</span></span></span> "<em>Skin pigmentation related variants in Mexican population and interaction effects on serum 25(OH)D concentration and vitamin D deficiency</em>".</p> <p> </p>
FIG. 1. — A, deux variantes d in Biodiversité des vers de terre (Annelida, Clitellata) des milieux cultivés des Antilles françaises
FIG. 1. — A, deux variantes d'une organisation des soies lombricine. À gauche, coupe transversale et vue ventrale de rangées de soies étroitement appariées (huit ventrales); à droite, coupe transversale et vue ventrale de rangées de soies très écartées (quatre ventrales et quatre latérales); B, coupe transversale et vue ventrale d'une organisation des soies périchaetine.
Plasma metabolomic signatures for copy number variants and COVID-19 risk loci in Northern Finland Populations
<p>A MySQL database for metabolomic signatures for The Northern Finland Birth Cohorts, <strong>NFBC1966 </strong>and <strong>NFBC1986</strong>, a longitudinal research program based at the Medical Faculty, University of Oulu, Finland. This dataset is a supplement to the manuscript titlted "Plasma metabolomic signatures for copy number variants and COVID-19 risk loci in Northern Finland Populations"</p>
3D full atom models of A501X variants of the penicillin-binding protein 2 with ceftriaxone
<p>The archives containPDB structures.</p> <p> <br>b3-b4-loop-representative-states.7z -- representative states obtained in MD trajectories of A501X variants of the PBP2</p> <p>The rest archves, A501X.7z contain representative frames from QM/MM MD trajectories in the stationary point regions (ES, TS1, I1, TS2, EP). Both QM part only and full-atom rectangular periodic systems are presented.</p> <p> </p>
Epigenetic-gene-variant-dynamics-analysis
<p>The dataset and analysis pipeline provided here are part of the study titled "Mapping Epigenetic Gene Variant Dynamics: Comparative Analysis of Frequency, Functional Impact, and Trait Associations in African and European Populations." This study investigates the frequency and functional impact of genetic variants in epigenetic genes across different populations, focusing on African and European ancestries. The files included are essential for replicating the analysis described in the manuscript. Key files include data from the GWAS Catalog and phenotype from the Pan-UK Biobank study and the UK Biobank, facilitating the investigation of trait associations with epigenetic variants. The complete code and description of additional data files necessary for the analysis can be accessed on GitHub at<span> </span><a href="https://github.com/smsinks/epigenetic-gene-variant-dynamics-analysis" target="_new">https://github.com/smsinks/epigenetic-gene-variant-dynamics-analysis</a>.</p>
16S Amplicon sequence variants (ASVs) data of NEREA Augmented Observatory
<p><strong>Metabarcoding - 16S ASV generation and taxonomic assignment</strong>. Raw 16S paired-end sequences were subjected to a data quality control step and subsequently imported into the QIIME2 pipeline v.2022.2.0. Leftover primers and adapter sequences were removed through cutadapt. The amplicon sequence variants (ASV) table, which represent true biological sequences within each sample, was generated using the denoised-paired method including truncation, denoising, dereplication, merging, and chimera filtering of the DADA2 (Divisive Amplicon Denoising Algorithm 2) plugin inside QIIME2. Default parameters were used with the exception of the forward and reverse sequence length (--p-trunc-len-f and --p-trunc-len-r), that were set to 220 and 180, respectively. Processed reads that passed all these filters were used for taxonomy classification. The V4-V5 regions were extracted from the pre-formatted reference sequences and taxonomy file built on the SILVA 138 99% OTUs database and the vsearch v.2.6.2 global alignment implemented in QIIME2 was used.</p>
Electron microscopy images and morphometric data of SARS-CoV-2 variants in ultrathin plastic sections - Dataset 05 (SARS-CoV-2 Delta B.1.617.2)
<p>Dataset 05 comprises 153 transmission electron microscopy images of extracellular SARS-CoV-2 (isolate Delta B.1.617.2) particles in ultrathin plastic sections (45 nm) through Vero cell cultures. The images were recorded with dimensions of 4112 x 3008 pixels at a pixel size of 0.1641 nm and stored in 16-bit TIF format. It is recommended that an image viewer capable of reading 16-bit images, such as IrfanView, be used to visualize the images. The image files have been size calibrated and can be opened with the correct size calibration using ImageJ or Fiji with the Bioformats importer. A PDF document is provided with the image files, which describes the methods used for the generation of the images. Additionally, an XLSX file is included, offering morphometric particle measurements and the calculated statistical values for their distribution. The dataset was produced as dataset 05 for a comparative morphometric analysis of evolving SARS-CoV-2 variants. Further datasets used for the analysis are available in this repository (see dataset description document).</p>
Electron microscopy images and morphometric data of SARS-CoV-2 variants in ultrathin plastic sections - Dataset 03 (SARS-CoV-2 Alpha B.1.1.7)
<p>Dataset 03 comprises 147 transmission electron microscopy images of extracellular SARS-CoV-2 (isolate Alpha B.1.1.7) particles in ultrathin plastic sections (45 nm) through Vero cell cultures. The images were recorded with dimensions of 4112 x 3008 pixels at a pixel size of 0.1641 nm and stored in 16-bit TIF format. It is recommended that an image viewer capable of reading 16-bit images, such as IrfanView, be used to visualize the images. The image files have been size calibrated and can be opened with the correct size calibration using ImageJ or Fiji with the Bioformats importer. A PDF document is provided with the image files, which describes the methods used for the generation of the images. Additionally, an XLSX file is included, offering morphometric particle measurements and the calculated statistical values for their distribution. The dataset was produced as dataset 03 for a comparative morphometric analysis of evolving SARS-CoV-2 variants. Further datasets used for the analysis are available in this repository (see dataset description document).</p>
Electron microscopy images and morphometric data of SARS-CoV-2 variants in ultrathin plastic sections - Dataset 01 (SARS-CoV-2 Munich929)
<p>Dataset 01 comprises 150 transmission electron microscopy images of extracellular SARS-CoV-2 (isolate Munich929) particles in ultrathin plastic sections (45 nm) through Vero cell cultures. The images were recorded with dimensions of 4112 x 3008 pixels at a pixel size of 0.1641 nm and stored in 16-bit TIF format. It is recommended that an image viewer capable of reading 16-bit images, such as IrfanView, be used to visualize the images. The image files have been size calibrated and can be opened with the correct size calibration using ImageJ or Fiji with the Bioformats importer. A PDF document is provided with the image files, which describes the methods used for the generation of the images. Additionally, an XLSX file is included, offering morphometric particle measurements and the calculated statistical values for their distribution. The dataset was produced as dataset 01 for a comparative morphometric analysis of evolving SARS-CoV-2 variants. Further datasets used for the analysis are available in this repository (see dataset description document).</p>
Training material for Calling variants in non-diploid systems
<p>The majority of life on Earth is non-diploid and represented by prokaryotes, viruses and their derivatives such as our own mitochondria or plant’s chloroplasts. In non-diploid systems allele frequencies can range anywhere between 0 and 100% and there could be multiple (not just two) alleles per locus. The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between sequencing noise (abundant in all NGS platforms) and true low frequency variants. </p>
The population genetics of structural variants in grapevine domestication
<p><strong>The genome assembly: </strong><a href="https://zenodo.org/api/files/988c0749-aec9-42fe-865e-b09b140e2068/Chardonnay.fa.fasta?versionId=86a512b8-12a6-4f4d-ac5d-acc26d74589f">Chardonnay.fa.fasta</a> </p> <p><strong>The gene annotation: </strong><a href="https://zenodo.org/api/files/988c0749-aec9-42fe-865e-b09b140e2068/Chardonnay.annotation_sorted.gff.gz?versionId=2e5878bc-cf53-489b-ac71-2602f9ba4d2e">Chardonnay.annotation_sorted.gff.gz</a></p> <p><strong>The TE annotation: </strong><a href="https://zenodo.org/api/files/988c0749-aec9-42fe-865e-b09b140e2068/Chardonnay.annotation_te_sorted.gff3.gz?versionId=95780497-e0e7-4a7b-8860-74072d7f7bb2">Chardonnay.annotation_te_sorted.gff3.gz</a></p>
GCTB sparse shrunk LD matrices from 2.8M common variants from the UK Biobank - Part AC
<p>GCTB sparse shrunk LD matrices from 2.8M common variants from the UK Biobank.</p> <p>Part <strong>AC </strong>of AA, AB, AC, AD and AE</p>
GCTB sparse shrunk LD matrices from 2.8M common variants from the UK Biobank - Parts AD and AE
<p>GCTB sparse shrunk LD matrices from 2.8M common variants from the UK Biobank.</p> <p>Part <strong>AD </strong>of AA, AB, AC, AD and AE</p>
Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives
<p>This file contains the data we collected and analyzed in the paper <a href="https://www.frontiersin.org/articles/10.3389/fgene.2019.00914/abstract">https://www.frontiersin.org/articles/10.3389/fgene.2019.00914/abstract</a>. </p>
Comprehensive Structural Variant Benchmark Dataset: 1100 VCF files from long-read sequencing of 10 NCBI individuals
<p>We initially collected 10 NCBI individuals: HG002 family pedigree data (HG002 [son], HG003 [father], HG004 [mother]), the HG005 family pedigree data (HG005 [son], HG006 [father], HG007 [mother]), the NA12878 subject, the HG00096 subject, the HG00512 subject and the CHM13 subject. Then we used PacBio (CLR: Continuous Long Read, CCS: Circular Consensus Sequencing) and Nanopore (ONT) platforms, 5 aligners and 10 callers to construct the pipelines, with most parameters set to default values. After that, except for 6 invalid pipelines(pbmm2-Nanovar, lra-Picky, lra-delly, lra-NanoVar, lra-NanoSV, lra-pbsv), we obtain 1100 VCF files.</p>
Data set for the manuscript 'Leveraging pleiotropy identifies common-variant associations with selective IgA deficiency'
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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.