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29,145 results for “Association”
False discovery rate calculations for genome-wide association study of reproductive fitness in Drosophila melanogaster (Sussex LHM sample)
<p>R code and results of applying false discovery (FDR) rate calculations to establish statistical signficance in a genome-wide association study of reproductive fitness in Drosophila melanogaster. Phenotype values were generated on hemiclone female and male lines from an outbred, laboratory adapted population. Thus, GWAS were previously performed seperately on the phenotype values for each sex, and also using a bivariate GWAS implemented in the R package multiPhen.</p> <p>FDR calculations were performed using the R package 'fdrtool' on all SNPs, and on LD-independent SNPs, the latter of which was used to determine p-value thresholds for genome-wide significance when all SNPs were considered.</p> <p>This version differs from the original in that: i) Some gene positions/names have been reassigned for accuaracy in the input data. ii) A file containing the p-value thresholds corresponding to an FDR of 0.1 has been added. The 95% credible intervals for each SNP association have been added to the results data files.</p>
A longitudinal study of the associations of children's body mass index and physical activity with blood pressure – dataset
<p>B-Proact1v is a longitudinal study examining changes in children’s physical activity and sedentary behaviours as they progress through primary school. In 2012-2013, 1299 Year 1 children (median age: 6 years) were recruited from 57 schools in greater Bristol, UK (total number of eligible children: 2600; recruitment rate: 50.0%). Following this, data were collected from 1223 Year 4 children (median age: 9 years) from 47 of the original schools between March 2015 and July 2016 (total number of eligible children: 2047; recruitment rate: 59.7%). This included 685 children from the original sample.</p> <p> </p> <p>This dataset represents a subset of the B-Proact1v data to examine the longitudinal associations of children’s body mass index and physical activity with blood pressure. Included in this repository is the dataset and a data dictionary. The dataset includes the variables that underlie the findings in a manuscript entitled ‘A longitudinal study of the associations of children’s body mass index and physical activity with blood pressure’ that has been submitted to PLOS ONE. This dataset has been made available so that future researchers can replicate the study findings using the data. If you wish to use the data for any purpose other than replicating the study findings, please contact the Principal Investigator Professor Russ Jago (russ.jago@bristol.ac.uk) to discuss this.</p>
The C-terminus of the oncoprotein TGAT is necessary for plasma membrane association and efficient RhoA-mediated signaling
<p>The figures and raw data that are presented in the paper "<strong>The C-terminus of the oncoprotein TGAT is necessary for plasma membrane association and efficient RhoA-mediated signaling</strong>"</p>
Knowledge of Social Networks for Health is Associated with COVID-19 Health Protective Behaviors
<p>This is the dataset and stata code for the paper "Knowledge of Social Networks for Health is Associated with COVID-19 Health Protective Behaviors” submitted to Plos One May 1st, 2024.</p>
Genotypes for Neurospora nested association mapping population
<p>Genotype file that contains genotypes all the Neurospora association mapping population developed in Kronholm lab. See https://github.com/ikron/Neurospora_NAM_population</p> <p>The file is a tab-delimited text file in hapmap format and contains first contains the columns: rs alleles chrom pos strand assembly center protLSID assayLSID panel GCcode and then the subsequent columns are strains identifiers. The column 'rs' is the name of the SNP, column 'alleles' shows which two alternative bases occur, the column 'chrom' is the chromosome, column 'pos' is the coordinate, columns 'strand', 'center', 'protLSID', 'assayLSID', 'panel' and 'GCcode' contain all missing data. They are included for hapmap format compatibility. The column 'assembly' indicates the version of the Neurospora crassa reference genome that the coordinates are based on. And in this case it is NC12 for all SNPs.</p> <p>Missing data is indicated by 'N'</p>
Joint AstraZeneca-Cancer Research Horizons Functional Genomics Centre's CRISPRn library benchmark screens: gRNA counts and associated metadata
<p>Genome-wide CRISPR sgRNA libraries have emerged as transformative tools to systematically probe gene function. While these libraries have been iterated over time to be more efficient, their large size limits their use in some applications. Here, we benchmarked publicly available genome-wide single-targeting sgRNA libraries and evaluated dual targeting as a strategy for pooled CRISPR loss-of-function screens. We leveraged this data to design two minimal genome-wide human CRISPR-Cas9 libraries that are 50% smaller than other libraries and that preserve specificity and sensitivity, thus enabling broader deployment at scale. </p>
Paired Vegetation and Soil Burn Severity Metrics and Associated Climate, Weather, Topographical, and Land Cover Attributes
<p>This dataset pairs differenced Normalized Burn Ratio (dNBR) and soil burn severity (SBS) for 254 large (>400 ha in size) fires across the western US. Dataset also includes climate, weather, topography, physical and chemical soil characteristics, and land cover attributes of each burned pixel at the time of fire. This effort provided a table of 16.3 million burned pixels and their associated characteristics including dNBR, SBS, and 94 biological and physical covariates. After removing correlated features, the final data includes 18 fire covariates namely: dNBR, elevation, slope, aspect, land cover type, wind speed, energy release component, vapor pressure deficit, annual precipitation, and annual average daily max temperature, as well as the clay, sand and silt content of the soil and volumetric fraction of coarse fragments and soil organic carbon content. We also included spatial coherence metrices for dNBR, including DVAR, SHADE and SAVG. This data is provided as CSV files in Xtrain, Xvalidation, Xtest, as well as Ytrain, Yvalidation, and Ytest; in which X files (model input) provide all features except for SBS and Y files (model output) include SBS.</p><p>We also provided this data for an additional 16 large fires across the western US ("Extra Test" folder, including Dataset – X file – and Label – Y file).</p><p>Finally, the trained XGBoost model to translate dNBR to SBS using the associated features is also provided in this folder.</p>
Improved visualization of oral microbial consortia- Associated images
<p>These images are associated to the paper <strong>"Improved visualization of oral microbial consortia" published in the Journal of Dental Research.</strong></p> <p>Sample author: Tabita Ramirez Puebla</p> <p>Images show microbial consortia from human tongue dorsum biofilm.</p> <p>Imaged in a confocal microscope (Zeiss LSM 780) with a spectral detector (32 channels).</p> <p>Objective: Plan-Apochromat 63X; N.A. 1.4; Oil </p> <p>Pixel size: 0.07 um x 0.07 um</p> <p>Image size (pixels): 2048 x 2048</p> <p>Optical section : 1 micron</p> <p> </p> <p><strong>File descriptions</strong></p> <p><strong>TIFF files in Image5D format. Files resulted from linear unmixing performed with Zeiss ZEN algorithm (ZEN Black) or using the non-linear least-squares function in MATLAB. Individual fluorophore and autofluorescence channels are presented. </strong><br>Fig2A_5D<br>Fig2C_5D<br>Fig4_zstack_5D (zstack with 12 optical slices)</p> <p><strong>jpg files of pseudocolored images</strong><br>Fig2A_jpeg<br>Fig2B_jpeg<br>Fig2C_jpeg<br>Fig2D_jpeg<br>Fig3A_jpeg_stack_RGB_tif (stack of 257 optical slices RGB images in tif format)<br>Fig3A_Montage20x13_jpeg (Montage of 257 optical slices)<br>Fig3B_jpeg<br>Fig3C_jpeg<br>Fig3D_jpeg<br>Fig4A_xy (view of xy plane)<br>Fig4A_xz_orthogonal (view of xy plane -> orthogonal representation of 12 optical slices)<br>Fig4A_yz_orthogonal (view of yz plane -> orthogonal representation of 12 optical slices)<br>Fig4B_jpeg<br>Fig4C_jpeg</p> <p><strong>Representative Zeiss .czi (raw files from LSM780 confocal microscope)</strong><br>Fig2A_raw (original czi file)<br>Fig2C_raw (original czi file)</p>
Community science approach reveals temporal and eutrophication-related spatial patterns in bladderwrack-associated invertebrate fauna
<p>Data related to the "Community science approach reveals temporal and eutrophication-related spatial patterns in bladderwrack-associated invertebrate fauna" paper by Salo, Nieminen, Salovius-Laurén and Rinne published in Estuarine, Coastal and Shelf Science in 2024. <a href="https://doi.org/10.1016/j.ecss.2024.108822">https://doi.org/10.1016/j.ecss.2024.108822</a></p> <p>The data describes the community data collected with the community science method described in the paper. </p>
Dataset associated with Banks et al.: "Dust aerosol from the Aralkum Desert influences the radiation budget and atmospheric dynamics of Central Asia"
<p>This dataset contains the COSMO-MUSCAT simulation output for the 'Dustbelt' (DUBLT) scenarios of Central Asian dust aerosol and associated radiative effects described by the paper "Radiative cooling and atmospheric perturbation effects of dust aerosol from the Aralkum Desert in Central Asia", written by Banks et al. and submitted to ACP in 2023. The paper was renamed "Dust aerosol from the Aralkum Desert influences the radiation budget and atmospheric dynamics of Central Asia" in 2024.</p>
Supplementary Material for "Invasive plants are associated with increased fire frequency but decreased burn severity in Southern California shrubland ecosystems"
<p>This Zenodo repository contains all data, scripts, and supplementary materials for the manuscript entitled, "Invasive plants are associated with increased fire frequency but decreased burn severity in Southern California shrubland ecosystems".</p>
Assessment of skin autofluorescence and its association with glycated hemoglobin, cardiovascular risk markers and concomitant chronic diseases in children with type 1 diabetes
<p>This is the dataset for the publication "Assessment of skin autofluorescence and its association with glycated hemoglobin, cardiovascular risk markers and concomitant chronic diseases in children with type 1 diabetes".</p>
Variant dataset and code for "Population-level whole genome sequencing of Ascochyta rabiei identifies genomic loci associated with isolate aggressiveness"
<p>This dataset contains genetic variants (SNPs) of <em>Ascochyta rabiei</em> isolates and the R code used in their analysis to generate the results and figures described in the manuscript "<strong>Population-level whole genome sequencing of <em>Ascochyta rabiei</em> identifies genomic loci associated with isolate aggressiveness</strong>".</p> <div> <div> </div> </div>
DEM and associated kinematic GPS coordinates of September 2002 survey of the salar de Uyuni, Bolivia
<p>This dataset consists of two parts: 1) the post-processed kinematic GPS coordinates of a September 2002 survey of a 45 x 54 km region of the salar de Uyuni, Bolivia. 2) a digital elevation model (DEM) of the salar de Uyuni surface derived from those kinematic GPS data.</p> <p>Details of the survey and DEM generation can be found in the manuscript, "Topography of the salar de Uyuni, Bolivia from kinematic GPS" (doi: 10.1111/j.1365-246X.2007.03604.x). The only difference between this dataset and one described is that the DEM was generated from fitting two-dimensional Fourier basis set with parameters: L_x = L_y = 70000 meters, m = n = 10. This results in a basis set with a nominal resolution of 7 km, which is almost identical to that used in the dataset shown in the manuscript.</p>
Data for "Excitation of Low- and High-frequency Magnetosonic Whistler Waves Associated with SLAMS in the Terrestrial Foreshock" by Yao et al.
<p>The database includes the plasma data used in instability analyses and the theoretical analysis results based on the linear model.</p> <h3>Captions:</h3> <div><strong>Plasma_input.mat</strong> file is the plasma data used in the instability analyses, which is used to plot Figure 2a-2d.</div> <ul> <li><strong><em>B</em></strong>: magnetic field strength</li> <li><strong><em>n</em></strong>: plasma number density</li> <li><strong><em>Te_para</em></strong>: parallel electron temperature</li> <li><strong><em>Te_perp</em></strong>: perpendicular electron temperature</li> <li><strong><em>Tp</em></strong>: proton temperature</li> </ul> <div> </div> <div><strong>WWs_theo_predictions.mat</strong> file is the calculation result of linear growth rate and wave frequency. The results are used to plot Figure 2e and 2f.</div> <ul> <li><strong><em>f_theo</em></strong>: wave frequency in theoretical predictions</li> <li><strong><em>gamma_theo</em></strong>: growth rate in theoretical predictions</li> </ul>
Data associated with Altermagnetic superconducting diode effect
<p>Dataset for paper: Altermagnetic Diode Effect (https://arxiv.org/abs/2402.14071)</p>
Two-time correlation function based on speckle patterns from x-ray photon correlation spectroscopy associated with "Intermittent cluster dynamics and temporal fractional diffusion in a bulk metallic glass" (scientific article published in Nature Communications, 2024)
<p>This dataset consists of contrast data, i.e., the two-time correlation function, based on speckle patterns measured at the at the 8ID-E beamline of the Advanced Photon Source at Argonne National Laboratory.</p> <p>Experimental details are stated in the paper specified under "related work" and in the accompanying supplementary information.</p> <p>You are welcome to use this dataset in compliance with the CC BY 4.0 licence assigned to this dataset.</p> <p>Any questions regarding the data can be addressed to birte.riechers@bam.de who would also appreciate a note if you find the data useful.</p> <p>____________________________________________________________________</p> <p>The data consists of 32 text files in total, which correspond to the main and lower panel Figure 2 of the main publication. </p> <p>30 of these text files are contrast data, which are named "contrast_DT250s_nn.text" wiith "nn" as the identifier of consecutive data sets going from 1 to 30. Each data set consists of p rows and q columns, DT250s denotes the time resolution of data points, which is 250 s along both row and column values.</p> <p>The data set called "Time_Contrast_1to30s.txt" states the start time in seconds of the first data point of each of the thirty contrast data set.</p> <p>The data set called "ScatteredIntensity.txt" states the scattered intensity at full time resolution, i.e. 2.5 s.</p> <p>The files are plain text files with the data points separated by "space" along rows and "new line" along columns.</p>
Structural basis of actin monomer re-charging by cyclase-associated protein
<p>1) table_of_simulations.pdf: table of simulations</p> <p>2) toppar_HIC.str: methylhistidine (HIC) topologies and parameters</p> <p> -prepared based on analogy</p> <p> -to be used with top_all36_prot.rtf and par_all36_prot.prm</p> <p>3) simulation_archive.tar.gz</p> <p> The Contents:</p> <p>1_ADP-Actin--CARP, 2_ADP-Actin--CAP1, 3_ATP-Actin--WH2, 4_ADP-Actin<br> All systems presented in the paper; see table_of_simulations.pdf<br> Each directory contains<br> 000README gromacs_topologies gromacs_tpr_files index.ndx processed_trajectories prod.mdp systems_at_t=0</p> <p>*** The rosetta models for WH2 domain and the proline-rich loop that connects it to the CARP domain can be found in 2_ADP-Actin--CAP1/rosetta_models</p> <p><br> _Topologies:<br> toppar_c36_jul16:<br> The charmm force field version used to generate topologies before conversion to gromacs; see 000README in the systems directory<br> <br> ***toppar_c36_jul16/toppar_HIC.str: The topology and parameters for methylated histidine used in the simulations.</p> <p> gromacs_topologies:<br> Contains all itp files (converted from psf file using PyTopol's psf2top utility) and parameters.<br> Note that relevant files can also be found in directories corresponding to each system ( 1_ADP-Actin--CARP 2_ADP-Actin--CAP1 3_ATP-Actin--WH2 4_ADP-Actin)</p> <p> </p>
CryoEM Models and Associated Data Submitted to the 2015/2016 EMDataBank Model Challenge
<p>Files and metadata associated with the EMDataBank/Unified Data Resource for 3DEM 2015/2016 Models Challenge hosted at challenges.emdatabank.org are deposited.</p> <p>All members of the Scientific Community--at all levels of experience--were invited to participate as Challengers, and/or as Assessors.</p> <p>Eight recently determined target structures were selected for the challenge. All of the maps were archived in the EM Data Bank (EMDB; http://emdatabank.org).</p> <p>In total 16 Challengers created 106 models and uploaded their results with associated details. In the zip files, each entry is represented in a folder containing the original deposition upload (deposited_EM.pdb), initial processing at RCSB/Rutgers (deposited_EM_edited.pdb, maxit.cif, maxit.cif.pdb) and final model version evaluated (model-compare.pdb) at UC Davis (http://model-compare.emdatabank.org).</p> <p>This model challenge was one of two community-wide challenges sponsored by EMDataBank in 2015/2016 to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model.</p> <p> </p>
Genome-wide association summary statistics for varicose veins of lower extremities
<p>The dataset contains summary statistics for the discovery and the replication stages of the large-scale genome-wide associations study for varicose veins of lower extremities. The discovery stage was based on genetic association data provided by the Neale Lab (<a href="https://vk.com/away.php?to=http%3A%2F%2Fwww.nealelab.is%2F&cc_key=">http://www.nealelab.is/</a>) for 337,199 UK biobank individuals. Phenotype “varicose veins of lower extremities” was defined based on International Classification of Disease (ICD-10) billing code “I83” present in the electronic patient record. Data were adjusted for two potential confounders – body mass index and deep venous thrombosis. A replication cohort (N=71,256) was generated by means of reverse meta-analysis of two overlapping datasets: genetic association data for 408,455 UK Biobank participants provided by the Gene ATLAS database (<a href="https://vk.com/away.php?to=http%3A%2F%2Fgeneatlas.roslin.ed.ac.uk%2F&cc_key=">http://geneatlas.roslin.ed.ac.uk/</a>), and the above mentioned data provided by the Neale Lab.</p> <p>Please, note, that in Shadrina et al (PLOS Genetics 2019) we only used "discovery" dataset, while in biorxiv preprint (https://doi.org/10.1101/368365) both discovery and replication datasets were used. </p> <p>The data are provided on an "AS-IS" basis, without warranty of any type, expressed or implied, including but not limited to any warranty as to their performance, merchantability, or fitness for any particular purpose. If investigators use these data, any and all consequences are entirely their responsibility. By downloading and using these data, you agree that you will cite the appropriate publication in any communications or publications arising directly or indirectly from these data; for utilisation of data available prior to publication, you agree to respect the requested responsibilities of resource users under 2003 Fort Lauderdale principles; you agree that you will never attempt to identify any participant. </p> <p><strong>When using downloaded data, please cite corresponding paper and this repository:</strong></p> <ol> <li> <p>Shadrina, A. S., Sharapov, S. Z., Shashkova, T. I. & Tsepilov, Y. A. Varicose veins of lower extremities: Insights from the first large-scale genetic study. <em>PLOS Genet.</em> <strong>15,</strong> e1008110 (2019).</p> </li> <li>Alexandra S. Shadrina, Sodbo Zh. Sharapov, Tatiana I. Shashkova, & Yakov A. Tsepilov. (2018). Genome-wide association summary statistics for varicose veins of lower extremities (Version 1) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1323484</li> </ol> <p><strong>Funding:</strong></p> <p>The work of ASS was supported by the Russian Science Foundation [Project No 17-75-20223]. <br> The work of YAT was supported by the Russian Ministry of Science and Education under the 5-100 Excellence Programme. <br> The work of SZS was supported by the Institute of Cytology and Genetics [Project No 0324-2018-0017].</p> <p><strong>Column headers - discovery</strong></p> <ol> <li>SNP: SNP rsID</li> <li>b: effect size of effect allele</li> <li>se: standard error of effect size</li> <li>chi2: T^2 value of effect allele</li> <li>Pval: P-value of association (without GC correction)</li> <li>N: sample size</li> <li>Chr: chromosome</li> <li>Pos: position (GRCh37 build)</li> <li>A1: effect allele (coded as "1")</li> <li>A2: reference allele (coded as "0")</li> </ol> <p><strong>Column headers - replication</strong></p> <ol> <li>SNP: SNP rsID</li> <li>A1: effect allele (coded as "1")</li> <li>A2: reference allele (coded as "0")</li> <li>N: Total sample size</li> <li>Z: Z-value of effect allele</li> <li>P: P-value of association (without GC correction)</li> </ol>
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)
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DANDI Archive for NWB datasets
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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.