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1,985 results for “Antigen”
Association between diminished miRNA expression and acquired alterations of ABO antigen expression in leukemia patients
<p><strong>Supplementary Table S1.</strong> The clinical significance of miRNAs in acute leukemia.</p>
Learning Context-aware Structural Representations to Predict Antigen and Antibody Binding Interfaces
<p>These are data corresponding to the paper '<a href="https://doi.org/10.1093/bioinformatics/btaa263">Learning Context-aware Structural Representations to Predict Antigen and Antibody Binding Interfaces</a>', published in Bioinformatics 2020. The code to run the experiments can be found on github <a href="https://github.com/vamships/PECAN">here</a>.</p>
Data from: Global circulation patterns of seasonal influenza viruses vary with antigenic drift
Understanding the spatiotemporal patterns of emergence and circulation of new human seasonal influenza virus variants is a key scientific and public health challenge. The global circulation patterns of influenza A/H3N2 viruses are well characterized1, 2, 3, 4, 5, 6, 7, but the patterns of A/H1N1 and B viruses have remained largely unexplored. Here we show that the global circulation patterns of A/H1N1 (up to 2009), B/Victoria, and B/Yamagata viruses differ substantially from those of A/H3N2 viruses, on the basis of analyses of 9,604 haemagglutinin sequences of human seasonal influenza viruses from 2000 to 2012. Whereas genetic variants of A/H3N2 viruses did not persist locally between epidemics and were reseeded from East and Southeast Asia, genetic variants of A/H1N1 and B viruses persisted across several seasons and exhibited complex global dynamics with East and Southeast Asia playing a limited role in disseminating new variants. The less frequent global movement of influenza A/H1N1 and B viruses coincided with slower rates of antigenic evolution, lower ages of infection, and smaller, less frequent epidemics compared to A/H3N2 viruses. Detailed epidemic models support differences in age of infection, combined with the less frequent travel of children, as probable drivers of the differences in the patterns of global circulation, suggesting a complex interaction between virus evolution, epidemiology, and human behaviour.
A molecular basis for the presentation of phosphorylated peptides by HLA-B antigens (ANNOTATED MS2 SPECTRA OF PHOSPHOPEPTIDES)
<p>Phosphopeptides identified from the immunopeptidome of the C1R-B*40 cell line. </p> <p>Phosphopeptides identified from the proteome of the C1R-B*40 cell line. </p> <p>Phosphopeptides identified from the immunopeptidome of the GR cell line. </p>
Quality of vaccination-induced T cell responses is conveyed by polyclonality and high, but not maximum, antigen receptor avidity
<p>This repository contains the processed data of the single-cell T cell analysis connected to the manuscript "Diverse and balanced repertoires of high-functionality T cell receptors are induced by SARS-CoV-2 mRNA vaccination" from Kocher and Drost et al. </p> <p>The data is stored in the AnnData (Scanpy+Scirpy) format and can be reproduced with this GitHub repository (<a href="https://github.com/SchubertLab/CovidVac_CD8">https://github.com/SchubertLab/CovidVac_CD8/</a>) from the raw data stored under GEO accession numbers GSE261966, GSE261967, and GSE249998. </p> <p><span><span> </span></span></p>
Antibody-Antigen Models for McCoy 2024 Paper: "A Comparison of Antibody-Antigen Complex Sequence-to-Structure Prediction Methods and their Systematic Biases"
<p>Up to the top 20 models generated for each method tested in the 2024 Paper: "A Comparison of Antibody-Antigen Complex Sequence-to-Structure Prediction Methods and their Systematic Biases"</p>
Source data for: Human monoclonal antibodies against Staphylococcus aureus surface antigens recognize in vitro biofilm and in vivo implant infections
<p class="CxSpFirst">Implant-associated <i>Staphylococcus aureus</i> infections are difficult to treat because of biofilm formation. Bacteria in a biofilm are often insensitive to antibiotics and host immunity. Monoclonal antibodies (mAbs) could provide an alternative approach to improve the diagnosis and potential treatment of biofilm-related infections. Here we show that mAbs targeting common surface components of <i>S. aureus</i> can recognize clinically relevant biofilm types. The mAbs were also shown to bind a collection of clinical isolates derived from different biofilm-associated infections (endocarditis, prosthetic joint, catheter). We identify two groups of antibodies: one group that uniquely binds <i>S. aureus </i>in biofilm state and one that recognizes <i>S. aureus </i>in both biofilm and planktonic state. Furthermore, we show that a mAb recognizing wall teichoic acid (WTA; clone 4497) specifically localizes to a subcutaneously implanted pre-colonized catheter in mice. In conclusion, we demonstrate the capacity of several human mAbs to detect <i>S. aureus</i> biofilms<i> in vitro</i> and <i>in vivo</i>.</p>
Unaltered T cell responses to common antigens in individuals with Parkinson's disease--AIM Assay FCS (1.2/3)
<p>FCS files pertaining to the AIM analysis described and included in "Unaltered T cell responses to common antigens in individuals with Parkinson's disease". Part 1.2/3 of dataset, data key can be found in within 3/3 upload.</p>
Unaltered T cell responses to common antigens in individuals with Parkinson's disease--AIM Assay FCS Data (1/3)
<p>FCS files pertaining to the AIM analysis described and included in "Unaltered T cell responses to common antigens in individuals with Parkinson's disease". Part 1/3 of dataset, data key can be found in within 3/3 upload.</p>
Unaltered T cell responses to common antigens in individuals with Parkinson's disease--AIM Assay FCS (2/3)
<p>FCS files pertaining to the AIM analysis described and included in "Unaltered T cell responses to common antigens in individuals with Parkinson's disease". Part 2/3 of dataset, data key can be found in within 3/3 upload.</p>
TCR convergence is a indicator of antigen-specific T cell response in immunotherapies
<p>This compressed file contains all the convergent TCR sequence information involved in this study. </p>
CLEC-1 is a death sensor that limits antigen cross-presentation by dendritic cells and represents a target for cancer immunotherapy
<p>Tumors exploit numerous immune checkpoints including those deployed by myeloid cells to curtail anti-tumor immunity. Here, we show that the C-type lectin receptor CLEC-1 expressed by myeloid cells senses dead cells killed by programmed necrosis. Moreover, we identified TRIM21 as an endogenous ligand over-expressed in various cancers. Interestingly, we observed that in mice CLEC-1 blockade combined with chemotherapy to prolong survival in tumor models. Loss of CLEC-1 reduced the accumulation of immunosuppressive myeloid cells in tumors and invigorated the activation state of dendritic cells (DCs), thereby increasing T cell responses. Mechanistically, we found that the absence of CLEC-1 increased the cross-presentation of dead-cell associated antigens by conventional type-1 DCs. Importantly, we identified anti-human CLEC-1 antagonist antibodies able to enhance anti-tumor immunity in CLEC-1 humanized mice. Altogether, our results demonstrate that CLEC-1 acts as an immune checkpoint in myeloid cells and support CLEC-1 as a novel target for cancer immunotherapy.</p>
Multi-antigen imaging data of skin tissue samples from cutaneous T cell lymphoma, atopic dermatitis, and psoriasis patients
<h1>Data</h1> <p>Multi-antigen imaging data for 69 skin tissue samples (21 cutaneous T cell lymphoma (CTCL), 23 atopic dermatitis (AD), and 25 pseudolymphoma (PSO)), obtained from 27 patients (8 CTCL, 7 AD, 12 PSO) treated at the University Hospital Erlangen. Each sample contains at least 36 protein channels, each of resolution 512 X 512 pixels. The data were generated using multi-epitope ligand cartography (MELC) (https://doi.org/10.1038/nbt1250, https://doi.org/10.1007/3-540-36459-5_8).</p> <h1>Metadata</h1> <p>For each sample, we information on sex, age, and condition of the corresponding patient. Samples and patients are numbered as S01 through S69 and P01 through P27, respectively.</p> <h1>Structure of the repository</h1> <ul> <li>The file <strong>metadata.csv</strong> contains the metadata.</li> <li>The archive <strong>data.zip</strong> contains one directory for each sample, named with the sample numbers S01 through S69.</li> <li>The directories for the individual samples contain images named<strong> <marker>-<flourescent protein>.tif</strong>, where <marker> is the name of the quantified protein marker and <flourescent protein> is the name of the flourescent protein that was used for image acquisition.</li> </ul> <p> </p> <p> </p>
Non-coding regions are the main source of targetable tumor-specific antigens - DATASETS (k=24)
<p>Tumor-specific antigens (TSAs) represent ideal targets for cancer immunotherapy, but few have been identified thus far. We therefore developed a proteogenomic approach to enable the high-throughput discovery of TSAs coded by potentially all genomic regions. In two murine cancer cell lines and seven human primary tumors, we identified a total of 40 TSAs, about 90% of which derived from allegedly non-coding regions and would have been missed by standard exome-based approaches. Moreover, the majority of these TSAs derived from non-mutated yet aberrantly expressed transcripts (such as endogenous retroelements) that could be shared by multiple tumor types. In mice, the efficacy of TSA vaccination was influenced by two parameters that can be estimated in humans and could serve for TSA prioritization in clinical studies: TSA expression and the frequency of TSA-responsive T cells in the pre-immune repertoire. In conclusion, the strategy reported herein could considerably facilitate the identification and prioritization of actionable human TSAs.</p>
Non-coding regions are the main source of targetable tumor-specific antigens – DATASETS (k=33)
<p>Tumor-specific antigens (TSAs) represent ideal targets for cancer immunotherapy, but few have been identified thus far. We therefore developed a proteogenomic approach to enable the high-throughput discovery of TSAs coded by potentially all genomic regions. In two murine cancer cell lines and seven human primary tumors, we identified a total of 40 TSAs, about 90% of which derived from allegedly non-coding regions and would have been missed by standard exome-based approaches. Moreover, the majority of these TSAs derived from non-mutated yet aberrantly expressed transcripts (such as endogenous retroelements) that could be shared by multiple tumor types. In mice, the efficacy of TSA vaccination was influenced by two parameters that can be estimated in humans and could serve for TSA prioritization in clinical studies: TSA expression and the frequency of TSA-responsive T cells in the pre-immune repertoire. In conclusion, the strategy reported herein could considerably facilitate the identification and prioritization of actionable human TSAs.</p>
Single-cell analysis reveals host S phase drives large T antigen expression during BK polyomavirus infection
Open the record for dataset details and reuse information.
Resources of "Evolving antibody response to SARS-CoV-2 antigenic shift from XBB to JN.1"
<p>Resources of the article "Evolving antibody response to SARS-CoV-2 antigenic shift from XBB to JN.1". See https://github.com/yunlongcaolab/SARS-CoV-2-JN.1-mAbs for future updates.</p>
Analysis of RNA polymerase II clusters in fixed embryos injected with antigen-binding fragments
<p>Data and scripts for the analysis of RNA polymerase II clusters. The data set includes data obtained from fixed zebrafish embryos injected with antigen-binding fragments, CellProfiler pipelines for the initial analysis of images are provided, along with Python scripts to export data into CSV format and execute downstream analysis.</p>
Diagnostic accuracy of Panbio™ rapid antigen test for SARS-CoV-2 in paediatric population
<p>The aim was to evaluate the accuracy of the Panbio<sup>TM</sup> Rapid Antigen Test for SARS-CoV-2 in the setting of a primary health care centre (PHC) in paedriatic population, with use of the Reverse Transcription-Polymerase Chain Reaction (RT-PCR) as gold standard.</p>
Data for: Low protease activity in B cell follicles promotes retention of intact antigens after immunization
<p>The structural integrity of vaccine antigens is critical to the generation of protective antibody responses, but the impact of protease activity on vaccination in vivo is poorly understood. We characterized protease activity in lymph nodes and found that antigens were rapidly degraded in the subcapsular sinus, paracortex, and interfollicular regions, whereas low protease activity and antigen degradation rates were detected in the vicinity of follicular dendritic cells (FDCs). Correlated with these findings, immunization regimens designed to target antigen to FDCs led to germinal centers dominantly targeting intact antigen, whereas traditional immunizations led to much weaker responses that equally targeted the intact immunogen and antigen breakdown products. Thus, spatially compartmentalized antigen proteolysis affects humoral immunity and can be exploited.</p>
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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.