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934 results for “Bovines”
Genetic analysis of mycobacteria isolated from suspect bovine tuberculosis lesions in Wolaita, Ethiopia - code and datasets.
<p>Bovine tuberculosis (bTB), caused by Mycobacterium bovis and other members of the Mycobacterium tuberculosis complex (MTBC), is a significant concern for livestock and public health in Ethiopia. This study aimed to assess the prevalence and causative agents of bTB in cattle from four abattoirs in the Wolaita region of Ethiopia. </p>
Performance and agreement between WGS variant calling pipelines used for bovine tuberculosis control: towards international standardisation
<p>This repository contains the simulated genomes and FASTQ files used for the analyses reported in the publication: <strong>Performance and agreement between WGS variant calling pipelines used for bovine tuberculosis control: towards international standardisation</strong>.</p> <p>This dataset is based on previously published data: <a href="https://doi.org/10.1099/mgen.0.000388">https://doi.org/10.1099/mgen.0.000388</a></p> <p>Processing scripts can be found in: <a href="https://github.com/Viloleal/bTB-pipeline-comparison-data-and-tools">https://github.com/Viloleal/bTB-pipeline-comparison-data-and-tools</a></p>
FIG. 4 in De l'art d'engraisser les bovins dans le berceau de la Charolaise
FIG. 4. — Le champ de foire de Saint-Christophe-en-Brionnais dans les années 1930. Photo: collection personnelle Dominique Fayard.
Genotype of expression quantitative loci (eQTL) analyses for bovine blood and liver
<p>To identify expression quantitative loci (eQTL) operating in bovine blood and liver, 238 animals were genotyped uisng Illumina BovineHD genotyping arrary. For this file minor allele is used as ref as the default in plink.</p>
Data from: Effect of culling on individual badger Meles meles behaviour: potential implications for bovine tuberculosis transmission
Open the record for dataset details and reuse information.
Data from: A natural gene drive system influences bovine tuberculosis susceptibility in African buffalo: possible implications for disease management
Bovine tuberculosis (BTB) is endemic to the African buffalo (Syncerus caffer) of Hluhluwe-iMfolozi Park (HiP) and Kruger National Park, South Africa. In HiP, the disease has been actively managed since 1999 through a test-and-cull procedure targeting BTB-positive buffalo. Prior studies in Kruger showed associations between microsatellite alleles, BTB and body condition. A sex chromosomal meiotic drive, a form of natural gene drive, was hypothesized to be ultimately responsible. These associations indicate high-frequency occurrence of two types of male-deleterious alleles (or multiple-allele haplotypes). One type negatively affects body condition and BTB resistance in both sexes. The other type has sexually antagonistic effects: negative in males but positive in females. Here, we investigate whether a similar gene drive system is present in HiP buffalo, using 17 autosomal microsatellites and microsatellite-derived Y-chromosomal haplotypes from 401 individuals, culled in 2002-2004. We show that the association between autosomal microsatellite alleles and BTB susceptibility detected in Kruger, is also present in HiP. Further, Y-haplotype frequency dynamics indicated that a sex chromosomal meiotic drive also occurred in HiP. BTB was associated with negative selection of male-deleterious alleles in HiP, unlike positive selection in Kruger. Birth sex ratios were female-biased. We attribute negative selection and female-biased sex ratios in HiP to the absence of a Y-chromosomal sex-ratio distorter. This distorter has been hypothesized to contribute to positive selection of male-deleterious alleles and male-biased birth sex ratios in Kruger. As previously shown in Kruger, microsatellite alleles were only associated with male-deleterious effects in individuals born after wet pre-birth years; a phenomenon attributed to epigenetic modification. We identified two additional allele types: male-specific deleterious and beneficial alleles, with no discernible effect on females. Finally, we discuss how our findings may be used for breeding disease-free buffalo and implementing BTB test-and-cull programs.
Sex affects immunolabeling for histone 3 K27me3 in the trophectoderm of the bovine blastocyst but not labeling for histone 3 K18ac
<p>The mammalian embryo displays sexual dimorphism in the preimplantation period. Moreover, competence of the embryo to develop is dependent on the sire from which the embryo is derived and can be modified by embryokines produced by the endometrium such as colony stimulating factor 2 (CSF2). The preimplantation period is characterized by large changes in epigenetic modifications of DNA and histones. It is possible, therefore, that effects of sex, sire, and embryo regulatory molecules are mediated by changes in epigenetic modifications. Here it was tested whether global levels of two histone modifications in the trophectoderm of the bovine blastocyst were affected by sex, sire, and CSF2. It was found that amounts of immunolabeled H3K27me3 were greater (P=0.030) for male embryos than female embryos. Additionally, labeling for H3K27me3 and H3K18ac depended upon the bull from which embryos were derived. Although CSF2 reduced the proportion of embryos developing to the blastocyst, there was no effect of CSF2 on labeling for H3K27me3 or H3K18ac. Results indicate that the blastocyst trophoctoderm can be modified epigenetically by embryo sex and paternal inheritance through alterations in histone epigenetic marks.</p>
A bovine molQTL cohort for three reproductive tissues
<p>Transcriptome and whole-genome sequence variant data for a cohort of 118 post-pubertal bulls, as well as GWAS summary statistics for a cohort of 3736 bulls.</p><p>This dataset contains gene abundance (in TPM, both raw and normalized estimates), splicing variation (from LeafCutter), and whole-genome sequence variants (raw, unfiltered) for 118 bulls. Gene abundance and splicing variation is available for three reproductive tissues (testis, epididymis, vas deferens). Autosomal, X-chromosomal, and MT genes are included.</p><p>All sample-IDs refer to ENA accession numbers. A cross-table (cohort_accession_numbers.xlsx) allows to assign transcriptome to genotype data.</p><p>The bovine ARS-UCD1.2 assembly and the corresponding Ensembl annotation (ftp://ftp.ensembl.org/pub/release-104/gtf/bos_taurus/Bos_taurus.ARS-UCD1.2.104.chr.gtf.gz) was used</p>
Deep microbiome-based characterization of the alterations in resident bacterial communities of pasteurized bovine milk contaminated with Salmonella Typhimurium over time
Open the record for dataset details and reuse information.
Fig. 1 in Systematic review of modifiable risk factors shows little evidential support for most current practices in Cryptosporidium management in bovine calves
Fig. 1 Study selection procedure
Microbiological monitoring results for bovine and ovine carcass production in Australia.
Open the record for dataset details and reuse information.
Improved estimation of the prevalence of bovine cysticercosis and the diagnostic test characteristics in the absence of a reference standard using Bayesian Latent Class models, the example of Jimma and Ambo Abattoirs, Ethiopia
<p>Bovine cysticercosis is an infection of cattle musculature with the cestode parasite of humans known as Taenia saginata. This bovine cysticercosis data was collected from two Ambattoirs in Ethiopia namely Ambo and Jimma. Dissection of the predilection site, Ag-ELISA, and meat inspection were the diagnostic methods employed. Cysticerci collected during dissection of the predilection site were also confirmed using multiplex PCR. </p>
Bovine tuberculosis model for England and Wales (BoTMEW) including model description.
<p>This model is a research tool, which has been released to allow confirmation of model outputs referred to by a paper published in BMC Veterinary Research <a href="http://em.rdcu.be/wf/click?upn=lMZy1lernSJ7apc5DgYM8X-2BU0XJX47KPodALuc5i6bY-3D_OFgvmg1J6naJevMotmPmRq4kYgQ8qSNe-2B7zZNGv6ek02fVecAo7cYwhzLqyA3UrbV6-2FZ3SxptJRsuip92JxM0XFtAQWr5IIYhumLNYchiGTCH-2FbT2bRLcXeRxtcW3cVfxE1koKeOOrp9lcfO6TZgafkYfbuQN6x3d2CY3FQFlr728vT4Wq5Oou9A8SSWGXkIw1gzin24Wx1PNPwbP9xQxH9SJpHs-2FLlYsaqck5RIdtYIfcC5WNJlx4kQQo0lXlXOvOlB5a42hEgZsaQ1HAtxzQ-3D-3D">https://rdcu.be/5NcV</a>. Outputs are only suitable for evaluating the behaviour of the model. The model is not recommended for any other use. Although the overall distribution of cattle herds represents cattle herds in England and Wales during 2008-2010, all individual herd identities are fictional.</p> <p>This dataset has been made available under an Open Government License 3.0. The model uses open access code libraries under licenses that are provided in the file "license.txt".</p> <p>This is the bovine tuberculosis model for England and Wales (BoTMEW), including a model description, and a zip file to download, including executable, parameter and set up files for baseline simulations 2008 - 2022.</p> <p>The model simulates bovine tuberculosis throughout England and Wales at the resolution of individual farms and infected cattle. However, this version is anonymized below county level, so it can only generate outputs at county resolution.</p> <p>The model set up includes a complete anonymized listing of cattle movements to match the model for 2008 - 2010.</p> <p>Full details of the model specification and set up are presented in the document "ModelDescriptionv5.6.pdf", in the most recent version of this upload.</p> <p>The zip includes actual outputs from 10 replicate simulations of the baseline model setup. It also includes a .ods workbook at its top level, which demonstrates how model fit in 2010 was calculated using those outputs.</p>
Number of bovine animals tested by age group, reporting country and target group, 2018
<p>The tables contain the number of bovine animals tested by age group, reporting country and target group, 2018</p>
FIG. 2 in De l'art d'engraisser les bovins dans le berceau de la Charolaise
FIG. 2. — Pays naisseurs, pays d'embouche. Carte: Dominique Fayard
FIG. 1 in De l'art d'engraisser les bovins dans le berceau de la Charolaise
FIG. 1. — Situation de la région étudiée. Carte: Dominique Fayard.
Metabolome data from bovine preovulatory follicular fluid
<p class="MsoNormal">The intrafollicular milieu influences mammalian fertility by providing the microenvironment for oocyte growth and maturation. A number of studies have linked abundance of follicular fluid metabolites to oocyte developmental competence and pregnancy outcome. Few studies have interrogated the preovulatory follicular fluid metabolome in cattle. This dataset includes preovulatory follicular fluid metabolome profiles from non-lactating Jersey cows. Ultra-High-Performance Liquid Chromatography-High Resolution Mass Spectrometry was performed on preovulatory follicular fluid samples and Xcalibur (RAW) files were converted to an open-source mzML format (msconvert software; ProteoWizard package). The converted files were processed using the Metabolomic Analysis and Visualization Engine (MAVEN; mzroll software, Princeton University) to complete an untargeted analysis of the liquid chromatography mass spectrometry data. The pre-processed peak data tables generated by MAVEN are provided in this dataset. </p>
Supplementary Material to the Publication: Clonal relation between Salmonella enterica subspecies enterica serovar Dublin strains of bovine and food origin in Germany
<p>OHEJP Project: BeOne</p> <p><em>Salmonella enterica </em>serovar Dublin (<em>S</em>. Dublin) is a host-adapted serovar that causes enteritis and/or systemic diseases in cattle. Because the serovar is not host-specific, it can infect other species, including human beings, causing severe disease and a higher mortality rate than other non-typhoidal serovars. Given that human illnesses are primarily caused by contaminated milk, milk products, and beef, data on the genetic connection between <em>S</em>. Dublin strains from livestock and food should be analyzed. </p> <p>Whole genome sequencing (WGS) was performed on 144 <em>S</em>. Dublin strains from cattle and 30 strains from food. Multilocus sequence typing (MLST) found that the majority of livestock and food isolates were of the sequence type ST-10. As discovered by core-genome Single-Nucleotide Polymorphisms Typing and core-genome MLST, 14 of 30 strains from food origin were clonally related to at least one strain from cattle. Without outliers, the remaining 16 food-borne strains fit into the genomic structure of <em>S</em>. Dublin in Germany. WGS demonstrated to be an effective method not only for learning about the epidemiology of Salmonella strains, but also for detecting clonal relationships between organisms isolated at different stages of production. This study discovered a strong genetic link between <em>S</em>. Dublin strains from cattle and food, and thus the potential to cause human infections. <em>S</em>. Dublin strains from both origins have a nearly comparable collection of virulence factors, emphasizing their ability to produce severe clinical symptoms in animals as well as humans, emphasizing the importance of effective <em>S</em>. Dublin management in a farm to fork strategy.</p>
Supplemental data for "Transcriptomic Profiling of the Bovine Endosalpinx and Endometrium to Identify Putative Embryokines"
<p>Supplemental data for paper describing expression of genes encoding for cell-signaling ligands in the oviduct and endometrium of cows. </p>
BEACH Trial: Bovine Early Access, Compatibility and Hemostasis Trial
ClinicalTrials.gov study NCT04146012. IPD Sharing: NO. Countries: 1. Publications: 3.
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)
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.