Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
2,212
datasets available to search
ShareScore release 0.9.0
Dataset results
2,212 results for “virality”
Uncovering hundreds of RNA viral RdRps amongst uncharacterised sequences in public protein databases.
<p>These data are associated with the following manuscript:</p> <p>Brown, K., Firth, A. E. (2025)<br>Uncovering hundreds of RNA viral RdRps amongst uncharacterised sequences in public protein databases.<br><br></p>
BRONQUIOLITE VIRAL AGUDA: UMA REVISÃO BIBLIOGRÁFICA
<p>A Bronquiolite Viral Aguda (BVA) é a infecção predominante no trato respiratório inferior em lactentes e crianças até dois anos de idade, sendo caracterizada pelo primeiro episódio de sibilância associado a uma infecção viral. O Vírus Sincicial Respiratório (VSR) é o principal agente causal em 80-85% dos casos, seguido por outros vírus como parainfluenza, adenovírus e influenza. A manifestação respiratória é variada, geralmente começando com um período prodrômico de 2-3 dias, apresentando sintomas semelhantes a uma síndrome gripal comum, como tosse seca, coriza clara e espirros.</p>
A distinct isoform of lymphoid enhancer binding factor 1 (LEF1) epigenetically restricts EBV reactivation to maintain viral latency
<p>As a human tumor virus, EBV is present as a latent infection in its associated malignancies where genetic and epigenetic changes have been shown to impede cellular differentiation and viral reactivation. We reported previously that levels of the Wnt signaling effector, lymphoid enhancer binding factor 1 (LEF1) increased following EBV epithelial infection and an epigenetic reprogramming event was maintained even after loss of the viral genome. Elevated LEF1 levels are also observed in nasopharyngeal carcinoma and Burkitt lymphoma. To determine the role played by LEF1 in the EBV life cycle, we used in silico analysis of EBV type 1 and 2 genomes to identify over 20 Wnt-response elements, which suggests that LEF1 may bind directly to the EBV genome and regulate the viral life cycle. Using CUT&RUN-seq, LEF1 was shown to bind the latent EBV genome at various sites encoding viral lytic products that included the immediate early transactivator BZLF1 and viral primase BSLF1 genes. The LEF1 gene encodes various long and short protein isoforms. siRNA depletion of specific LEF1 isoforms revealed that the alternative-promoter derived isoform with an N-terminal truncation (∆N LEF1) transcriptionally repressed lytic genes associated with LEF1 binding. In addition, forced expression of the ∆N LEF1 isoform antagonized EBV reactivation. As LEF1 repression requires histone deacetylase activity through either recruitment of or direct intrinsic histone deacetylase activity, siRNA depletion of LEF1 resulted in increased histone 3 lysine 9 and lysine 27 acetylation at LEF1 binding sites and across the EBV genome. Taken together, these results indicate a novel role for LEF1 in maintaining EBV latency and restriction viral reactivation via repressive chromatin remodeling of critical lytic cycle factors.</p>
Generative AI in the Advancement of Viral Therapeutics for Predicting and Targeting Immune-Evasive SARS-CoV-2 Mutations
<p>This dataset <strong>encompasses</strong> and describes the following features:</p> <ul> <li>Mutations in viruses like SARS-CoV-2 can make them escape vaccines and treatments.</li> <li>Accurately predicting these mutations is crucial for developing effective countermeasures.</li> <li>The study uses a type of AI called a Generative Adversarial Network (GAN) to analyze the virus's spike protein, which plays a key role in infection.</li> <li>The GAN generates protein sequences similar to natural ones, but which are also likely to evade immune responses.</li> <li>By analyzing these generated sequences, the researchers improve their AI model's ability to predict real-world escape mutations.</li> <li>This improved prediction could help design better vaccines and treatments, and prepare for future viral threats.</li> </ul>
Data and Analyses for Host plant-mediation of viral transmission and its consequences for a native butterfly
<p>This contains R code for all analyses and creation of figures included in the publication entitled "Host plant-mediation of viral transmission and its Q1 consequences for a native butterfly". This article has now been accepted for publication under DOI: 10.1002/ecy.4282. The files containing the data analysis script have been updated to reflect the final analyses included in this paper. </p>
Data for: Viral receptor-binding protein evolves new function through mutations that cause trimer instability and functional heterogeneity
<p>When proteins evolve new activity, a concomitant decrease in stability is often observed because the mutations that confer new activity can destabilize the native fold. In the conventional model of protein evolution, reduced stability is considered a purely deleterious cost of molecular innovation because unstable proteins are prone to aggregation and are sensitive to environmental stressors. However, recent work has revealed that non-native, often unstable protein conformations play an important role in mediating evolutionary transitions, raising the question of whether instability can itself potentiate the evolution of new activity. We explored this question in a bacteriophage receptor binding protein (RBP) during host-range evolution. We studied the properties of the RBP of bacteriophage before and after host-range evolution and demonstrated that the evolved protein is relatively unstable and may exist in multiple conformations with unique receptor preferences. Through a combination of structural modeling and in vitro oligomeric state analysis, we found that the instability arises from mutations that interfere with trimer formation. This study raises the intriguing possibility that protein instability might play a previously unrecognized role in mediating host-range expansions in viruses.</p>
Structural models of viral proteins described in Krupovic M, et al., Proc Natl Acad Sci U S A. 2024
<p>This archive contains structural models in PDB format described in Krupovic M, Kuhn JH, Fischer MG, Koonin EV. Natural history of eukaryotic DNA viruses with double jelly-roll major capsid proteins. Proc Natl Acad Sci U S A. 2024</p>
Autoimmunity-associated allele of tyrosine phosphatase gene PTPN22 enhances anti-viral immunity
<p>The 1858C>T allele of the tyrosine phosphatase <em>PTPN22</em> is present in 5-10% of the North American population and is strongly associated with numerous autoimmune diseases. Although research has been done to define how this allele potentiates autoimmunity, the influence <em>PTPN22</em> and its pro-autoimmune allele have in anti-viral immunity remains poorly defined. Here, we use single-cell RNA-sequencing and functional studies to interrogate the impact of this pro-autoimmune allele on anti-viral immunity during Lymphocytic Choriomeningitis Virus clone 13 (LCMV-cl13) infection. Mice homozygous for this allele (PEP-619WW) clear the LCMV-cl13 virus whereas wildtype (PEP-WT) mice cannot. This is associated with enhanced anti-viral CD4 T cell responses and a more immunostimulatory CD8a<sup>-</sup> cDC phenotype. Adoptive transfer studies demonstrated that PEP-619WW enhanced anti-viral CD4 T cell function through virus-specific CD4 T cell-intrinsic and extrinsic mechanisms. Taken together, our data show that the pro-autoimmune allele of <em>Ptpn22</em> drives a beneficial anti-viral immune response thereby preventing what is normally a chronic virus infection.</p>
RNA viral reference database
<p><span>The RNA viral reference database was composed of (1) 6,621 complete RNA viral genomes collected from the NCBI virus database (accessed on August 12<sup>th</sup>, 2022, [1]), (2) 378,253 RNA viral contigs from the RVMT database (v3)[2], and (3) 858 RNA viral genomes published in a terrestrial RNA viral study [3].</span></p> <p><span>[1] NCBI virus database, accessible at https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/</span></p> <p><span>[2] <span>Neri U, Wolf YI, Roux S, Camargo AP, Lee B, Kazlauskas D, Chen IM, Ivanova N, Allen LZ, Paez-Espino D.<strong><span> </span></strong>2022. Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell 185:4023-4037. e18.</span></span></p> <p><span>[3] <span>Chen Y-M, Sadiq S, Tian J-H, Chen X, Lin X-D, Shen J-J, Chen H, Hao Z-Y, Wille M, Zhou Z-C.<strong><span> </span></strong>2022. RNA viromes from terrestrial sites across China expand environmental viral diversity. Nature Microbiology 7:1312-1323.</span></span></p>
Seagrass associated viral genomes
<p>High-quality viral sequences associated with:</p> <p>A genomic resource for exploring bacterial-viral dynamics in seagrass ecosystems</p> <p>Analysis, code, intermediate and supporting files are archived here: <a href="https://doi.org/10.5281/zenodo.14226514">10.5281/zenodo.14226514</a></p> <p>Bacterial metagenome-assembled genomes from this work are archived here: <a href="https://doi.org/10.5281/zenodo.14225974" target="_blank" rel="noopener">10.5281/zenodo.14225974</a><br><br>This archive contains:<br>(i) Fasta file representing the 354 viral sequences in the final catalog described in the above titled work<br>(ii) Metadata file describing the viral catalog (i.e., Table S2 from the above work)</p>
A data repository for the study of Alpha-synuclein aggregates trigger anti-viral immune pathways and RNA editing in human astrocytes
<p><span>This repository contains data associated with the study:</span></p> <p><span><strong>"Alpha-synuclein Aggregates Trigger Anti-Viral Immune Pathways and RNA Editing in Human Astrocytes"</strong></span></p> <p><span>Published as a <strong>bioRxiv preprint</strong>: <a href="https://doi.org/10.1101/2024.02.26.582055"><span>DOI: 10.1101/2024.02.26.582055</span></a></span></p>
Additional data repository for the study of Alpha-synuclein aggregates trigger anti-viral immune pathways and RNA editing in human astrocytes
<p>Zip file 1: astrocytes calcium data measured using Fura 2</p> <p>Zip file2: astrocytes ROS measured using DHE (Dihydroethidium)</p> <p>Zip file 3: astrocytes cell death measured using Sytox green</p>
Principles of RNA recruitment to viral ribonucleoprotein condensates in a segmented dsRNA virus
<p><strong>Rotaviruses transcribe eleven distinct protein-coding RNAs that must be stoichiometrically co-packaged prior to their replication to make an infectious virion. During infection, </strong><strong>rotavirus transcripts accumulate in cytoplasmic ribonucleoprotein (RNP) condensates, termed viroplasms. </strong><strong>Understanding the mechanisms of viroplasm assembly and RNA enrichment within is crucial to gaining greater insight into their function and stoichiometric assortment of individual transcripts.</strong> <strong>We analysed the subcellular distribution of individual RV transcripts and viroplasm transcriptome by combining multiplexed DNA-barcoded single-molecule RNA FISH of infected cells. Using DNA-PAINT microscopy, we provide evidence of the early onset of viral transcript oligomerisation that occurs prior to the formation of viroplasms. We demonstrate that viral sequences lacking the conserved terminal regions fail to undergo enrichment in rotavirus RNP condensates. We show that individual viral transcripts exhibit variable propensities to partition into viroplasms, irrespective of their absolute numbers in cells, suggesting a selective RNA enrichment mechanism distinct from other known cellular RNP granules. </strong><strong>We suggest that rotavirus replication factories represent unique RNP condensates enriched in eleven types of cognate transcripts that may facilitate the assembly of a multi-segmented RNA genome.</strong></p>
Codes and parameter datasets for the "Bacteriophage self-counting in the presence of viral replication"
<p>Matlab codes and datasets used for modeling in the paper "Bacteriophage self-counting in the presence of viral replication" PNAS 2021 Vol. 118 No. 51 e2104163118 https://doi.org/10.1073/pnas.2104163118 </p>
Raw data to: "Vectored antibody gene delivery restores host B and T cell control of persistent viral infection"
<p>Raw data underlying the publication by Ertuna et al. entitled "Vectored antibody gene delivery restores host B and T cell control of persistent viral infection"</p>
Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection
<p><strong>scRNA-seq data</strong></p> <p>Data were processed using cellranger v 4.0.0 with the refdata-gex-GRCh38-2020-A reference.</p> <p><em>h5files.zip</em>: contains all h5-Files of raw feature-barcode counts (e.g. 20094_0001_A_B_raw_feature_bc_matrix.new.h5 )</p> <p><em>raw_feature_bc_matrices.zip</em>: contains the <em>same data</em> as h5files.zip, but also in mtx-format.</p> <p>covid_object_ncomms<em>.RDS</em>: contains the Seurat file with which all analyses were conducted.</p> <p><em>samples2condition.df</em>: text file containing sample to condition information</p> <p><strong>Bulk RNA-seq</strong></p> <p><em>covid_bulk.zip</em> contains the count matrices extracted from the zUMIs runs for the bulk cohort.</p> <p><em>nasal_swabs.zip</em> contains the count matrices extracted from the zUMIs run for the nasal swab cohort.</p> <p>The extracted count matrices were then used with the bulk analysis scripts provided with the source code.</p> <p><strong>Source Code</strong></p> <p>All <strong>source code</strong> for the publication is available from: <a href="https://github.com/mjoppich/covidSC">https://github.com/mjoppich/covidSC</a> or from tagged releases: <a href="https://github.com/mjoppich/covidSC/releases/tag/ncomms">https://github.com/mjoppich/covidSC/releases/tag/ncomms</a></p> <p>When using any of these data, please cite:<br> <br> Pekayvaz et al., Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection, Nature Communications 2022</p>
Raw data for the article: Successful Use of Heterologous CMV-Reactive T Lymphocyte to Treat Severe Refractory Cytomegalovirus (CMV) Infection in a Liver Transplanted Patient: Correlation of the Host Antiviral Immune Reconstitution with CMV Viral Load and CMV miRNome
<p>Cytomegalovirus (CMV) infection is the most significant viral infection in hosts with compromised immune systems as solid organ transplant patients. Despite significant progress being made in the prevention of CMV disease in these patients, further therapeutic strategies for CMV disease and for the CMV reactivation prevention are needed. Here, we describe the outcome of the infusion of in vitro expanded CMV-reactive T-cells, taken from a healthy CMV-seropositive donor, in a liver-transplanted recipient with a refractory recurrent CMV. In this particular case, adoptive transfer of allogenic CMV-reactive T-lymphocytes resulted in the clearance of CMV infection and resolution of the pathological manifestations of the patient. In the study we also investigated circulating miRNAs, both cellular and viral, as potential biomarkers during the course of CMV infection. The results indicate that the infusion of allogenic CMV-reactive T-cells can be an effective strategy to treat CMV infection recurrence when the generation of autologous virus specific T cell clones is not possible.</p>
Freshwater viral metagenome assembled genomes (vMAGs) used for vContact2 analysis in publication Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and nitrogen cycling in river sediments
<p>This dataset contains all freshwater viruses that were mined from publicly available data in an effort to provide biogeographical context to viral communities identified from the Columbia River. These two files include data from:</p> <p>1) East River, CO (PRJNA579838)</p> <p>2) A previous study from the Columbia River, WA (PRJNA375338)</p> <p>3) Prairie Potholes, ND (PRJNA365086)</p> <p>4) Amazon River (PRJNA237344)</p> <p> </p> <p>Manuscript title Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and nitrogen cycling in river sediments</p>
Datasets for: The HIV-1 viral protease is activated during assembly and budding prior to particle release
<p>HIV-1 encodes a viral protease that is essential for the maturation of infectious viral particles. While protease inhibitors are effective antiretroviral agents, recent studies have shown that prematurely activating – rather than inhibiting – protease function leads to the pyroptotic death of infected cells, with exciting implications for efforts to eradicate viral reservoirs. Despite 40 years of research into the kinetics of protease activation, it remains unclear exactly when protease becomes activated. Recent reports have estimated that protease activation occurs minutes to hours after viral release, suggesting that premature protease activation may be challenging to induce efficiently. Here, combining a powerful FRET-based assay to monitor viral protease activity with sensitive techniques including nanoscale flow cytometry and instant structured illumination microscopy, we demonstrate that the viral protease is activated within cells prior to the release of free virions. Using genetic mutants that lock protease into a 'precursor' conformation, we further show that both the precursor and mature protease have rapid activation kinetics and that the activity of the precursor protease is sufficient for viral fusion with target cells. Our finding that HIV-1 protease is activated within producer cells prior to release of free virions helps resolve a long-standing question of when protease is activated and suggests that only a modest acceleration of protease activation kinetics may be required to induce potent and specific elimination of HIV-infected cells.</p>
Synthetic viral samples with DVGs
<p>Two synthetic groups of fastq files with a known population of Defective Viral Genomes (DVGs) and the full genome virus. </p> <p>- 'sars216' dataset was generated from SARS-CoV-2 genome</p> <p>- 'tumv72' dataset was generated from Turnip Mosaic Virus.</p> <p>The composition of each file is defined in the composition file uploaded in the GitHub repository: https://github.com/MJmaolu/SyntheticSamplesWithDVGs.</p> <p>Simulated samples used to evaluate the performance of the DVGfinder tool (https://github.com/MJmaolu/DVGfinder).</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.