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2,880 results for “variant”
Filtered and annotated SNV and indel variants in the PC3 and LNCaP human prostate cancer cell lines
<p>150bp paired-end reads (insert size 350bp) were obtained using the Illumina HiSeqX sequencer. Samtools v1.3.1 mpileup and bcftools were used to interrogate indexed BAM files, from whole-genome reads aligned to human reference genome GRCh38 build 82, and generate a VCF (Variant Call Format) file of single nucleotide variants (SNVs) and short indel variants. Variants private, or unique to a particular cell line, or shared by both were next identified. Variants (likely to be common germline variants) present in HapMap, 1000 genomes phase 3 (2,504 human genomes), and the National Heart Lung and Blood Institute’s Exome Sequencing Project (ESP) (bundled variant data file available at https://goo.gl/mEogvD) were excluded. Variant files (VCF) were filtered using SnpSift with the following parameters: 'QUAL \textgreater= 200 \&\& DP \textgreater= 30', where QUAL denotes minimum variance confidence and DP total depth threshold. Filtered variants were annotated using SnpEff v4.3g. Please see https://github.com/sciseim/PCaWGS for associated scripts.</p> <p> </p>
Genomic variant data for the Jurkat cell line
<p>Variant calling data from whole-genome sequencing of the Jurkat cell line. The data set includes output files from four variant calling tools (jurkat_raw_variant_caller_output.tar.gz), final variant calls after filtering and merging the calls from the separate tools (jurkat_final_variant_calls.tar.gz), and files with variant effect information (jurkat_variant_effects.tar.gz).</p>
Data for "Using transmission Kikuchi diffraction to characterise alpha variants in an alpha+beta titanium alloy"
<p>This zipped folder contains data for "Using transmission Kikuchi diffraction to characterise alpha variants in an alpha+beta titanium alloy" published in Journal of Microscopy.</p> <p>The zipped folder contains:<br> - Phase map, where green regions are indexed as alpha Ti and red regions are indexed as beta Ti.<br> - IPF orientation maps along the X, Y and Z directions (with both phases combined).<br> - IPF colour keys for the alpha and beta phases.<br> - FSD micrographs at lower and higher magnification (not resized: one pixel per acquisition data point).<br> - TKD_Trial.ctf - text file describing orientations according to Bruker software conventions [1], as-exported from Bruker Esprit 2.1.<br> - TKD_BOR_MTEXplotter.m, an MTEX plotting tool which will plot orientations for this dataset (using MTEX version 4.3.2 installed on MATLAB 9.2 (R2017a)).</p> <p>[1] T.B. Britton, J. Jiang, Y. Guo, A. Vilalta-Clemente, D. Wallis, L.N. Hansen, A. Winkelmann, A.J. Wilkinson, Tutorial: Crystal orientations and EBSD — Or which way is up?, Materials Characterization, Volume 117, July 2016, Pages 113-126, ISSN 1044-5803, http://dx.doi.org/10.1016/j.matchar.2016.04.008.<br> (http://www.sciencedirect.com/science/article/pii/S1044580316300924)</p>
Experimental results of "Managing variant calling datasets the big data way"
<p>Tomatula was demonstrated for retrieving the allele frequencies for a given region in the data from Aflitos et al (2014). We developed scripts to retrieve allele frequencies, either from the VCF file storage or Apache Parquet. We executed a series of experiments, querying for a region of 2000 bases in the file of chromosome 6, that corresponds to the approximate length of a gene. We compared both storage formats (VCF files and Parquet), two input sizes (104 and 1144 individuals), different cluster sizes varying between 2 and 150 executor nodes, and HDFS replication factor was set to 3, 5, 7, and 9, in order to examine four main factors that<br> can affect the performance of a Big Data cluster: (a) the storage format, (b) the size of the input files, (c) the number of computing nodes of the cluster, and (d) the replication factor of HDFS. The block size of the HDFS was kept at the default value of 128MB. All experiments were executed five times and the detailed results are provided here, along with a script that produces the corresponding figures.</p>
Improved multi-ancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk
<p>sushie.molqtl.weights.tar.gz contains ancestry-specific eQTL and pQTL weights trained on mRNA and protein levels measured in American European, American African, and American Hispanic ancestries from TOPMed-MESA and GENOA studies. Column “a1” is the counting allele.</p> <p>mesa.*.fusion.tar.gz contains the weights in FUSION format.</p> <p>sushie_real_data_results.tar.gz contains all the real data analyzed in the sushie project.</p> <p>sushie_sim_data_results.tar.gz contains all the sim data analyzed in the sushie project.</p> <p>sushie_analysis_codes.tar.gz contains all the codes and scripts to generate and analyze these data.</p>
Example input and output files for the virus variant caller pipeline
<p><code>example_config_files.zip</code>: reference annotations for HSV-1 strain 17 and config files describing the input files.</p> <p><code>example_bam_files.zip:</code> alignment files (in BAM format) for two replicates each of the ICP0 and vhs knockout mutants.</p> <p><code>example_fastq_files.zip</code>: read sequences (in FASTQ format) for two replicates each of the ICP0 and vhs knockout mutants.</p> <p><code>example_output.zip</code>: resulting output files</p> <p> </p> <p>After downloading and unpacking the zip-archives, <strong>adjust the constants in the Watchdog workflow</strong> as follows:</p> <p><code><const name="REFERENCE">/path/to/chrHsv1_s17.fa</const></code><br><code><const name="REFERENCE_SNPS">/path/to/reference_snps.txt</const></code><br><code><const name="CONFIG">/path/to/config_strains_HSV1.txt</const></code><br><code><const name="GTF">/path/to/HSV1_Annotation_chrHsv1_s17.gtf</const></code><br><code><const name="samples">/path/to/example_samples.txt</const></code><br><code><const name="replicates">/path/to/example_replicates.txt</const></code></p> <p>where <code>/path/to/</code> is the directory the content of the archive zip-archives is located in.</p> <p>Furthermore, change <code>/path/to/</code> in the <code>example_replicates.txt</code> and <code>example_samples.txt</code> files to the directory the content of the archive zip-archives is located in.</p>
Identification of genetic variants associated with anterior cruciate ligament rupture and AKC standard coat color in the Labrador Retriever
<p>Canine anterior cruciate ligament (ACL) rupture is a common complex disease. Prevalence of ACL rupture is breed-dependent. In an epidemiological study, yellow coat color was associated with increased risk of ACL rupture in the Labrador Retriever. ACL rupture risk variants may be linked to coat color through genetic selection or through linkage with coat color genes. To investigate these associations, Labrador Retrievers were phenotyped as ACL rupture cases or controls and for coat color and were single nucleotide polymorphism (SNP) genotyped. After filtering, ~697K SNPs were analyzed using GEMMA and mvBIMBAM for multivariate association. Functional annotation clustering analysis with DAVID was performed on candidate genes. A large 8Mb region on chromosome 5 that included <em>ACSF3</em>, as well as 32 additional SNPs, met genome-wide significance at <em>P</em><6.07E-7 or Log<sub>10</sub>(BF) = 3.0 for GEMMA and mvBIMBAM, respectively. On chromosome 23, SNPs were located within or near <em>PCCB</em> and <em>MSL2</em>. On chromosome 30, a SNP was located within <em>IGDCC3</em>. SNPs associated with coat color were also located within <em>ADAM9</em>,<em> FAM109B</em>,<em> SULT1C4</em>,<em>RTDR1</em>,<em> BCR</em>, and <em>RGS7</em>. <em>DZIP1L</em> was associated with ACL rupture. Several significant SNPs on chromosomes 2, 3, 7, 24, and 26 were located within uncharacterized regions or long non-coding RNA sequences. This study validates associations with the previous ACL rupture candidate genes <em>ACSF3</em> and <em>DZIP1L</em> and identifies novel candidate genes. These variants could act as targets for treatment or as factors in disease prediction modeling. The study highlighted the importance of regulatory SNPs in the disease, as several significant SNPs were located within non-coding regions.</p>
Raw data for the association of genetic variants of ErbB4 gene and gestational diabetes mellitus
<div>Gestational diabetes (GDM) is one of the common complications of female pregnancy, which seriously affects the health of patients and their offspring. So far, the etiology has not yet been fully clarified. To clarify the relationship of Erb-b2 receptor tyrosine kinase 4 (ErbB4) genetic variants and GDM risk in a Chinese population, ErbB4 variants (rs1595064, rs1595065, rs1595066 and rs6719645) were selected and genotyped in 554 GDM cases and 641 healthy controls. The associations between variants and GDM risk were evaluated with the odds ratios (ORs) and their corresponding 95% confidence intervals (CIs). The false-positive reporting probability (FPRP), multi-factor dimension reduction (MDR) and bioinformatics analysis were adopted to confirm the significant associations. A nomogram model was constructed to predict the risk of GDM. Association analysis demonstrated that the rs1595066 genotype performed a protective effect on GDM risk among whole subjects. Meanwhile, stratified analysis showed that rs1595066 was significantly associated with GDM risk in various subgroups, such as age>30.09 years old, pre-pregnancy BMI>22.23 Kg/m<sup>2</sup> ,SBP≤110.08 mmHg, etc. Further, interactions between rs1595066 and DBP (Pinteraction=0.01), FPG (Pinteraction<0.001) and HbA1c (Pinteraction< 0.001) were detected. The FPRP analysis confirmed that association of rs1595066 and GDM risk in subjects of FPG≤4.79 mmol/L (P=0.199) is true at a prior probability of 0.1. The MDR analysis suggested that rs1595066 was the best single locus model, while the 4-loci model was considered the best multiple factors model to predict GDM risk. Functional prediction revealed that rs1595066 may disturb the microRNA binding sites to influence the stability of miRNA-mRNA binding. The predictive nomogram model has a good consistency and acceptable discriminative ability with a diagnosed AUC of 0.813.ErbB4 rs1595066 was significantly associated with GDM risk and underlying mechanism causing GDM may be the interaction of gene-gene, gene-environment and the changes in the regulatory effects of miRNAs on ERBB4 expression. The nomogram model has a good prospect for GDM prediction.</div>
Genetic variants regulating the immune response improve the prediction of COVID-19 severity provided by clinical variables
<p>Data set generated to evaluate the association between SNPs from genes related to SARS-CoV-2 pathogenesis and their clinical outcome.</p>
The Variant Prioritization Benchmark (VarPB)
<p>The Variant Prioritization Benchmark (VarPB) is an endeavor to create an open and freely-redistributable dataset for benchmarking variant pathogenicity prediction tools on a medical genetics task of prioritizing the pathogenic variant among all other variants in an individual. For more information, please visit the project website: https://zuchnerlab.github.io/VariantPrioritizationBenchmark/</p>
Data for: Genetic variants underlying human bisexual behavior are reproductively advantageous
<p>Because human same-sex sexual behavior (SSB) is heritable and leads to fewer offspring, how SSB-associated alleles have persisted and whether they will remain in human populations are of interest. Using the UK Biobank, we address these questions separately for bisexual behavior (BSB) and exclusive SSB (eSSB) after confirming their genetic distinction. We discover that male BSB is genetically positively correlated with the number of offspring. This unexpected phenomenon is attributable to the horizontal pleiotropy of male risk-taking behavior-associated alleles, because male risk-taking behavior is genetically positively correlated with both BSB and the number of offspring and because genetically controlling male risk-taking behavior abolishes the genetic correlation between male BSB and the number of offspring. By contrast, eSSB is genetically negatively correlated with the number of offspring. Our results suggest that male BSB-associated alleles are likely reproductively advantageous, which may explain their past persistence and predict their future maintenance, and that eSSB-associated alleles are likely being selected against at present.</p>
Genetic variants affecting NQO1 protein levels impact on efficacy of idebenone treatment in Leber hereditary optic neuropathy
<p>Fastq files with complete sequencing of NQO1 gene after PCR amplification for cell lines harboring m.11778G>A/MT-ND4 or m.3460A>G/MT-ND1 and controls.</p>
Variant calls for HG001-07
Open the record for dataset details and reuse information.
Smith Shinique - Bale Variant No. 0014
Clothing, fabric, paper, ribbon and found objects 2011, this 3D scan 2014 Scanned at: Museum of Fine Arts, Boston Source: Objaverse 1.0 / Sketchfab
Kugelarmband vom Typ Baden-Elsass Variante B
**Titel/Title**: Kugelarmband vom Typ Baden-Elsass Variante B **Objektbezeichnung/Description**: Armband **Inventarnummer/Accession Number**: C 4947 **Datierung/Date**: Eisenzeit, Hallstattzeit, Ha D1 (620-530 v. Chr.) **Orte/Locations**: Söllingen , Bannwald Hügel 2 (Fundort/Herkunft) **Material/Material**: Bronze **Technik/Manufacturing technique**: gepunzt, gegossen, geschmiedet **Maße/Size**: Gewicht: 595 g Höhe: 6.8 cm Breite: 10 cm Tiefe: 10.2 cm **Die 3D-Digitalisierungsstation wurde mit Mitteln der Klaus Tschira Stiftung finanziert.** Source: Objaverse 1.0 / Sketchfab
MD simulations from "#GotGlycans: Role of N343 Glycosylation on the SARS-CoV-2 S RBD Structure and Co-Receptor Binding Across Variants of Concern
<p>This folder contains all the MD simulations (saved in frames of 1 ns in PDB format) analysed and discussed in the paper titled "#GotGlycans: Role of N343 Glycosylation on the SARS-CoV-2 S RBD Structure and Co-Receptor Binding Across Variants of Concern" DOI https://doi.org/10.1101/2023.12.05.570076. The naming reflects the specific variant and the presence ('g' or 'gly') or absence ('ng' or 'nogly') of glycosylation at N343 and N331 sites in the SARS-CoV-2 S RBD. Gaussian accelerated MD simulations are indicated with 'gamd', all others represent conventional (deteriministic) sampling. For all details please refer to the original manuscript.</p>
Calling structural variants with confidence from short-read data in wild bird populations
<p>Comprehensive characterisation of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation (SV), reproducible and high-confidence SV callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (<em>Passer domesticus</em>) individuals. To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of SVs is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analysing short-read discovered SV datasets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality-filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence SV callsets.</p>
Multi-level in vivo selection of the biocontrol agent Akanthomyces muscarius, virulence, growth, sporulation, and variant data
<p>Changes in parasite virulence are commonly expected to lead to trade-offs in other life history traits that can affect fitness. Understanding these trade-offs is particularly important if we want to manipulate the virulence of microbial biological control agents. Theoretically, selection across different spatial scales, i.e. between- and within-hosts, shapes these trade-offs. However, trade-offs are also dependent on parasite biology. Despite their applied importance the evolution of virulence in fungal parasites is poorly understood: virulence can be unstable in culture and commonly fails to increase in simple passage experiments. We hypothesized that manipulating selection intensity at different scales would reveal virulence trade-offs in a fungal pathogen of aphids, <em>Akanthomyces muscarius</em>. Starting with a genetically diverse stock we selected for speed of kill, parasite yield, or infectivity by manipulating competition within and between hosts and between populations of hosts over 7 rounds of infection. We characterized ancestral and evolved lineages by whole genome sequencing and by measuring virulence, growth rate, sporulation, and fitness. While several lineages showed increases in virulence, we saw none of the trade-offs commonly found in obligately-killing parasites. Phenotypically similar lineages within treatments often shared multiple single-nucleotide variants, indicating strong convergent evolution. The most dramatic phenotypic changes were in the timing of sporulation and spore production <em>in vitro. </em>We found that early sporulation led to reduced competitive fitness but could increase the yield of spores on media, a trade-off characteristic of social conflict. Notably, the selection regime with the strongest between-population competition and lowest genetic diversity produced the most consistent shift to early sporulation, as predicted by social evolution theory. Multi-level selection therefore revealed social interactions novel to fungi and showed that these biocontrol agents have the genomic flexibility to improve multiple traits - virulence and spore production - that are often in conflict in other parasites.</p>
Dataset for research paper entitled Adaptive Phase or Variant Formation at the Austenite/Twinned Martensite Interface in Modulated Ni–Mn–Ga Martensite
<p><span>The dataset contains the experimental result concerning in-situ synchrotron and SEM/EBSD measurements as a function of temperature. The list of files is listed below:</span></p> <p><span>The dataset is composed of both the raw and processed data:</span></p> <p><strong><span>X-ray phase analysis</span></strong><span> - performed with a synchrotron radiation energy 87.1 KeV.</span></p> <ul> <li><span>Origin file 1 - Diffraction experiments made on NiMnGa single crystals below and above Ms temperature</span></li> <li><span>2D Diffraction pattern for 10M 10M’ Mt, and A structures.</span></li> </ul> <p><strong><span>TEM experiments</span></strong><span> - </span><span>Microstructural observations were carried out by ThermoFisher Scientific TitanThemis Cs corrected 200 kV scanning /transmission electron microscope (S/TEM) equipped with SuperX </span><a title="Learn more about EDX from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/materials-science/energy-dispersive-x-ray-spectroscopy"><span>EDX</span></a><span> detector system. Thin foil for analysis was prepared by </span><span>TEM observations were prepared with a TenuPol-5 double jet electropolisher using an electrolyte of nitric acid (70%) and methanol (30%) at -25 °C.</span></p> <p><span>· </span><span>File 1 set of HRTEM images showing modulation boundaries</span></p> <p><span>· </span><span>File 2 set of HRTEM images showing a/b boundaries</span></p> <p><strong><span>SEM/EBSD</span></strong><span> - </span><span>FEI Quanta 3D FEG SEM equipped with a TSL system and a Murano heating stage. To analyze the lattice parameter changes, a c</span><span>rystallographic analysis of lattice metric (CALM) was used. This method does not need a standard for indexing or lattice constant determination. The lattice metric (lattice parameters) was derived through the reconstruction of the experimental EBSD pattern. In the first step, centers of Kikuchi band traces were detected from the EBSD diffraction pattern. Then, using information about the diffraction projection center, 20 to 100 independent reflectors were reconstructed in the reciprocal space. The final step involves a search for primitive lattice vectors which are fulfilling translational symmetry conditions for all reflectors. Reconstructed vectors are recomputed to the higher symmetry lattices with a relative error lower than 0.1%</span><span>Thermogravimetric curves obtained for the decomposition of powder after synthesis at 500 rpm.</span></p> <ul> <li><span>Origin file 2 Relation between a/c lattice parameters</span></li> <li><span>Origin file 3 Relation between a/c lattice parameters</span></li> <li><span>SEM/BSE pictures showing austenite twinned/martensite interface</span></li> <li><span>Video 1 shows in-situ SEM/BSE with martensitic transformation and </span><span>one planar austenite/twinned martensite interface during cooling</span></li> <li><span>Video 2 shows set of Kikuchi pattern across Austenite martensite phase indicating elastic nature of the martensitic transformation</span></li> </ul>
Genomic Resources for BIC@MSKCC Mouse Variant Pipeline
<p>Custom genomic resource files for Mouse Variant pipeline. Details and code are here: https://github.com/soccin/MusVar</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.