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1,985 results for “Antigen”
Data for: Antigen footprint governs activation of the B cell receptor
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Data from: Sequence-based detection of emerging antigenically novel influenza A viruses
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Regression models generated by APRANK (computational prioritization of antigenic proteins and peptides from complete pathogen proteomes)
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A single-parasite transcriptional atlas of Toxoplasma gondii reveals novel control of antigen expression
Toxoplasma gondii, a protozoan parasite, undergoes a complex and poorly understood developmental process that is critical for establishing a chronic infection in its intermediate hosts. Here, we applied single-cell RNA-sequencing (scRNA-seq) on >5,400 Toxoplasma in both tachyzoite and bradyzoite stages using three widely studied strains to construct a comprehensive atlas of cell-cycle and asexual development, revealing hidden states and transcriptional factors associated with each developmental stage. Analysis of SAG1-related sequence (SRS) antigenic repertoire reveals a highly heterogeneous, sporadic expression pattern unexplained by measurement noise, cell cycle, or asexual development. Furthermore, we identified AP2 IX-1 as a transcription factor that controls the switching from the ubiquitous SAG1 to rare surface antigens not previously observed in tachyzoites. In addition, comparative analysis between Toxoplasma and Plasmodium scRNA-seq results reveals concerted expression of gene sets, despite fundamental differences in cell division. Lastly, we built an interactive data-browser for visualization of our atlas resource.
Development of a genus-specific antigen capture ELISA for orthopoxviruses. Target selection and optimized screening
<p><strong>Raw data for quantification of anti surface protein antibody binding to vaccinia virus.</strong></p> <p>Method description</p> <p>Immuno-negative staining and electron microscopy were performed as described elsewhere (Laue, 2010). Briefly, purified VACV<sub>NYCBOH</sub> particles were inactivated by incubation in freshly prepared 2% PFA in 0.05 M HEPES (pH 7.2), sonicated and immobilized on sample supports for transmission electron microscopy. Biotinylated pAbs were titrated on BSA coated grids, until detection with 5 nm gold nanoparticle coupled streptavidin (British Biocell, Cardiff, United Kingdom) resulted in the same mean background labelling density of ~10 particles per view field at a, 87,000-fold magnification (anti-A27: 0.7 µg/mL; anti-D8: 2 µg/mL; anti-H3: 0.9 µg/mL; anti-L1: 1.9 µg/mL). Negative staining was performed with either 0.1 or 0.5% uranyl acetate solution. For quantification, only IMV particles of the mulberry form, which were found isolated from other particles, were analyzed. Randomized sampling was done in 22 evenly distributed mesh areas with five viral particles analyzed per area. Imaging was done with a Tecnai 12 BioTwin (FEI Corp.) at 120 kV and a 1k digital CCD camera (Megaview III, Olympus Soft Imaging Solutions).</p>
Prostate specific antigen density values among patients with symptomatic prostatic enlargement in Nigeria
<p><strong>Background</strong></p> <p>This study aims to estimate the prostate specific antigen density(PSAD) cut off level for detecting prostate cancer( CAP) in Nigerian men with “grey zone PSA’’(4-10ng/ml) and normal digital rectal examination findings . We addressed this research question: Is the international PSAD cut off of 0.15 ideal for detecting CAP in our symptomatic patients with “grey zone PSA’’?</p> <p><strong> Methods</strong></p> <p>Aim: To estimate the prostate specific antigen density(PSAD) cut off level for detecting prostate cancer( CAP) in Nigerian men with “grey zone PSA’’(4-10ng/ml) and normal digital rectal examination findings .</p> <p>Design: prospective</p> <p>Setting: A tertiary medical center in Enugu Nigeria</p> <p> Participants: Two hundred and fifty four men with either benign prostatic hyperplasia (BPH) or prostate cancer (CAP) were recruited. </p> <p> Intervention: Patients with PSA above 4ng/ml or abnormal digital rectal examination or hypoecoic lesion in the prostate were biopsied.</p> <p>Outcome measures: PSAD and histology report of BPH or CAP</p> <p><strong>Results</strong></p> <p>Ninety seven patients had cancer of the prostate (CAP) while 157 has benign prostatic hyperplasia (BPH). Seventy two patients had their serum PSA value within the range of 4.0 and 10ng/ml . PSAD cut off level to detect CAP was 0.04(sensitivity 95.88 %; specificity 28.7 %).</p> <p> </p> <p><strong>CONCLUSION</strong> </p> <p>The PSAD cut off level generated for Nigerian men in this study is 0.04 which is relatively different from international consensus. This PSAD cut off level has a positive correlation with histology and could detect patients with CAP who have “grey zone PSA’’.</p>
Data from: Illuminating T cell-dendritic cell interactions in vivo by FlAsHing antigens
<p>Delineating the complex network of interactions between antigen-specific T cells and antigen presenting cells (APCs) is crucial for effective precision therapies against cancer, chronic infections, and autoimmunity. However, the existing arsenal for examining antigen-specific T cell interactions is restricted to a select few antigen-T cell receptor pairs, with limited in situ utility. This lack of versatility is largely due to the disruptive effects of reagents on the immune synapse, which hinder real-time monitoring of antigen-specific interactions. To address this limitation, we have developed a novel and versatile immune monitoring strategy by adding a short cysteine-rich tag to antigenic peptides that emits fluorescence upon binding to thiol-reactive biarsenical hairpin compounds. Our findings demonstrate the specificity and durability of the novel antigen-targeting probes during dynamic immune monitoring in vitro and in vivo. This strategy opens new avenues for biological validation of T-cell receptors with newly identified epitopes by revealing the behavior of previously unrecognized antigen-receptor pairs, expanding our understanding of T cell responses.</p>
Mapping SARS-CoV-2 antigenic relationships and serological responses
<p>During the SARS-CoV-2 pandemic, multiple variants escaping pre-existing immunity emerged, causing concerns about continued protection. Here, we use antigenic cartography to analyze patterns of cross-reactivity among a panel of 21 variants and 15 groups of human sera obtained following primary infection with 10 different variants or after mRNA-1273 or mRNA-1273.351 vaccination. We find antigenic differences among pre-Omicron variants caused by substitutions at spike protein positions 417, 452, 484, and 501. Quantifying changes in response breadth over time and with additional vaccine doses, our results show the largest increase between 4 weeks and >3 months post-2nd dose. We find changes in immunodominance of different spike regions depending on the variant an individual was first exposed to, with implications for variant risk assessment and vaccine strain selection.</p>
Two mosquito salivary antigens demonstrate promise as biomarkers of recent exposure to P. falciparum-infected mosquito bites
<p>Measuring malaria transmission intensity using the traditional entomological inoculation rate is difficult. Antibody responses to mosquito salivary proteins such as SG6 have previously been used as biomarkers of exposure to <em>Anopheles</em> mosquito bites. Here, we investigate four mosquito salivary proteins as potential biomarkers of human exposure to mosquitoes infected with <em>P. falciparum</em>: mosGILT, SAMPSP1, AgSAP, and AgTRIO. We tested population-level human immune responses in longitudinal and cross-sectional plasma samples from subjects with known <em>P. falciparum</em> infection from low and moderate transmission areas in Senegal using a multiplexed magnetic bead-based assay. AgSAP and AgTRIO were the best indicators of recent exposure to infected mosquitoes, with antibody responses to AgSAP in a moderate endemic area, and to AgTRIO in both low and moderate endemic areas, significantly higher than healthy non-endemic control cohort (p-values = 0.0245, 0.0064, and <0.0001 respectively). No antibody responses significantly differed between the low and moderate transmission area, or between equivalent groups during and outside the malaria transmission seasons. For AgSAP and AgTRIO, reactivity peaked 2-4 weeks after clinical <em>P. falciparum</em> infection and declined 3 months after infection. Reactivity to both AgSAP and AgTRIO peaked after infection and did not differ seasonally nor between areas of low and moderate transmission, suggesting reactivity is due to exposure to infectious mosquitos or recent biting rather than general mosquito exposure. Kinetics suggest reactivity is relatively short-lived. AgSAP and AgTRIO are promising candidates to incorporate into multiplexed assays for serosurveillance of population-level changes in <em>P. falciparum</em>-infected mosquito exposure.</p>
Pivotal role of O-antigenic polysaccharide display in the sensitivity against phage tail-like particles in environmental Pseudomonas kin competition
<p>Environmental pseudomonads<i> </i>colonize various niches including insect and plant environments. When invading these environments, bacteria are confronted with the resident microbiota. To cope with closely related strains they deploy narrow-spectrum weaponry such as tailocins, <i>i.e</i> phage tail-like particles. Little is known about the receptors for these tailocins especially among phylogenetically closely related species. Here, we studied the interaction between an R-tailocin from <i>Pseudomonas protegens </i>CHA0 and a targeted kin, <i>Pseudomonas protegens </i>Pf-5. Using genome-wide transposon insertion sequencing, we identified that lipopolysaccharides are involved in the sensitivity of Pf-5 towards the tailocin of CHA0. By generating Pf-5 lipopolysaccharide mutants and exposing them to extracted tailocin, we specified the two O-antigenic polysaccharides (O-PS) targeted by the tailocin. We affirmed the role of these O-PS through competition assays<i> in vitro </i>as well as in insects. Further, we demonstrate that O-PS are double-edge swords that are responsible for the sensitivity of <i>P. protegens</i> towards phage tail-like particles produced by their kin, but shield bacteria from the immune system of the insect. Our results shed light on the trade-off that bacteria are confronted with, where specific O-PS decorations can both be of benefit or disadvantage depending on the host environment and its bacterial inhabitants.</p>
SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8 T cells
<p>This dataset contains aggregated CellRanger output for six 10x Genomics (5'GEX+abTCR+Feature barcoding) experiments from the study by Minervina, Pogorelyy et al (<a href="https://www.medrxiv.org/content/10.1101/2021.07.12.21260227v3">medrxiv</a>). <br> The scripts to process it further are available at github (<a href="https://github.com/pogorely/COVID_vax_CD8">repository</a>). <br> Raw sequencing data is available at SRA (acc. PRJNA744851)</p>
Supplementary Data and Figures for "Myomedin replicas of gp120 V3 loop glycan epitopes of PGT121 and PGT126 antibodies as non-cognate antigens for HIV-1 broadly neutralizing antibodies"
<p>Supplementary pymol sessions for "Myomedin replicas of gp120 V3 loop glycan epitopes of PGT121 and PGT126 antibodies as non-cognate antigens for HIV-1 broadly neutralizing antibodies". Pymol sessions contain the source data for Figure 3, panels A-K.</p>
Data for: Immunogenicity of SARS-CoV-2 spike antigens derived from Beta & Delta variants of concern
<p>Using our strongly immunogenic SmT1 SARS-CoV-2 spike antigen platform, we developed novel antigens based on the Beta & Delta variants of concern. These antigens elicited higher neutralizing antibody activity to the corresponding variant than comparable vaccine formulations based on the original reference strain, while a multivalent vaccine generated cross-neutralizing activity to all three variants. This suggests that while current vaccines may be effective at reducing severe disease to existing variants of concern, variant-specific antigens, whether in a mono- or multivalent vaccine, may be required to induce optimal immune responses and reduce infection against arising variants.</p>
Supplementary data for article "Reduced B-cell antigenicity of Omicron lowers host serologic response"
<p>This repository contains five supplementary data files for the research article "<strong>Reduced B-cell antigenicity of Omicron lowers host serologic response</strong>". For more information, please refer to the article preprint https://doi.org/10.1101/2022.02.15.480546 and upcoming article at Cell Reports.</p> <p> </p> <ol> <li><strong>Table_hCoV229E.xlsx:</strong> list of hCoV229E RBD sequences, with associated isolate and collection date identifiers, and ScanNet antigenicity score for reproducing <strong>Figure 3A</strong>. Aligned sequences and templates are also provided.</li> <li><strong>table_artificial_variants.csv</strong>: List of artificial RBD sequences generated by an evolutionary-based sequence generative model for reproducing <strong>Figure 3B</strong>, <strong>Supplementary Figure S6H</strong>.</li> <li><strong>MSA_RBD.fasta:</strong> Multiple Sequence Alignment of RBD sequences and sample weights used for training the sequence generative model used in <strong>Figure 3B</strong>, <strong>Supplementary Figures S2C, S6</strong>.</li> <li><strong>table_antibody_hit_rate_RBD.csv</strong>: Empirical epitope distribution for the RBD, as determined from the Protein Data Bank and raw data for <strong>Supplementary Figure S1</strong>).</li> <li><strong>RBD_virtual_DMS.xlsx</strong>: virtual Deep Mutational Scan performed with ScanNet and the sequence generative model shown in <strong>Supplementary Figure S2</strong>.</li> </ol> <p> </p> <p> </p>
Antigen-specific memory NK cell responses against HIV and influenza utilize the NKG2/HLA-E axis
<p>For over a decade, multiple studies have disputed the notion of natural killer (NK) cells as purely innate lymphocytes by demonstrating that they are capable of putative antigen-specific immunological memory against multiple infectious agents including two critical global health priorities – human immunodeficiency virus (HIV) and influenza. However, the mechanisms underlying antigen specificity remain unknown. Herein, we demonstrate that antigen-specific human NK cell memory develops upon exposure to both HIV and influenza, unified by a conserved and epitope-specific targetable mechanism largely dependent on the activating CD94/NKG2C receptor and its ligand HLA-E, and confirm these findings by three rigorous assays. We validated the permanent acquisition of antigen-specificity by individual memory NK cells by single-cell cloning. We identified biomarkers of antigen-specific NK cell memory through complex immunophenotyping by 30-parameter flow cytometry showing elevated expression of KLRG1, a4b7, and NKG2C. Finally, we show individual HLA-E-restricted peptides that may constitute the dominant NK cell response in HIV-1- and influenza-infected persons in vivo. Our findings clarify the mechanisms behind antigen-specific memory NK cell responses, and suggest they could be targeted for future vaccines, cure strategies, or other therapeutic interventions.</p>
Streptococcus pyogenes pharyngitis elicits diverse antibody responses to key vaccine antigens influenced by the imprint of past infections.
<p>Here you will find the raw data (RawData.RData) and code (CHIVAS_SEROLOGY_Code.Rmd, an R Markdown file) for generating the analysis and figures for the following publication:</p> <p><strong><em>Streptococcus pyogenes</em> pharyngitis elicits diverse antibody responses to key vaccine antigens influenced by the imprint of past infections.</strong></p> <p>Joshua Osowicki1,2,3 #, Hannah R Frost1 #, Kristy I Azzopardi1, Alana L Whitcombe4, Reuben McGregor4, Lauren H. Carlton4, Ciara Baker1, Loraine Fabri1,5,6, Manisha Pandey7, Michael F Good7, Jonathan R. Carapetis8,9,10, Mark J Walker11,12,13, Pierre R Smeesters1,2,5,6, Paul V Licciardi2,14, Nicole J Moreland4 *, Danika L Hill15 *, Andrew C Steer1,2,3 *</p> <p>Provided in the RData file are the following items: </p> <p><strong>Dataframes: </strong></p> <p>"outcome" : clinical variables associated with human challenge for each participant</p> <p>"data" : ELISA and functional antibody responses for human challenge participants. Each timepoint and isotype for each antigen as seperate column)</p> <p>"data_long": Data equivalent to "data" file but in long format, i.e. One column for each antigen, timepoint and isotype as factors. </p> <p>"data.melt" : Data equivalent to "data" file but in longer format , i.e. timepoint, isotype and antigen as factors, 'value' as ELISA AU. </p> <p>"luminex" : IgG responses to 6 antigens analysed by luminex bead-based assay in human challenge participants.</p> <p>"luminex.children" : IgG responses to 6 antigen analysed by luminex bead-based assay in children</p> <p><strong>Vectors:</strong></p> <p>"pharyngitis" : participant "id" for the 19 individuals that developed pharyngitis. </p> <p>"Antigen.Order" : relates to "Main" antigen classification used in Figure 2</p> <p>'additional" : relates to "Additional </p> <p><strong>Function: </strong></p> <p>"custom_theme" : used as a theme when using ggplot to graph. </p> <p>Adobe Illustrator or Inkscape were used to generate the final image files for publication, with some graph editing to axes labels, font size, adding p-values etc. </p> <p> </p> <p><em><strong>Additional files: </strong></em></p> <p> 3 .csv files have been included for download</p> <p>"ELISA_data_wide_format.csv", a wide format data table of 25 human challenge individuals and 219 variables. Equivalent to the 'data' dataframe in the RData file</p> <p>"CHIVAS_luminex.csv", a long format data table of 25 human challenge participants at 1 week, 1 month, and 3 months. Equivalent to the 'luminex' dataframe in the RData file. </p> <p>"Luminex.children.csv", a datatable of 6 luminex variables for 39 children (healthy and post pharyngitis). Equivalent to the 'luminex.children' dataframe in the RData file. </p> <p> </p>
Targeting Plasmodium falciparum chondroitin sulfate a ligand: A highly conserved malaria antigen with potential for pregnancy-associated malaria vaccine development
<p>The dataset represents the details of sera samples collected from participants recruited for a longitudinal study. The sera was used for ELISA <em>in vitro</em> assays. The immunoreactivity of PfCSA-L antigen was assessed with the utilization of the gravidity status of the study participants. The antigen is used by the <em>plasmodium falciparum</em> parasite to adhere to the placenta during pregnancy and causes challenges both to the mother and her fetus.</p> <h5>Variables</h5> <ul> <li> <p>Sample_ID - This is the coded details of the study participant.</p> </li> <li> <p>Mean*od <em>_1st_visit, Mean</em>od <em>_2nd_visit, and Mean</em>od *_3rd_visit - These represent the mean reactivity values for antibody (IgG) to PfCSA-L antigen for antenatal visits 1,2 and 3 respectively.</p> </li> <li> <p>Gravida - Refers to the total number of confirmed pregnancies a female has had, regardless of the outcome of the pregnancy.</p> </li> <li> <p>PCR_Results - these are molecular diagnostic results for <em>Plasmodium falciparum</em> to assess whether the study participants were positive or negative for this species. positive = 1 and negative = 0</p> </li> <li> <p>Gestation..weeks - Refers to how far along the pregnancy is, from the first day of the woman's last menstrual cycle to the delivery</p> </li> <li> <p>Newborn outcome - Describes the health status of the childlren when they were born</p> </li> <li> <p>Gravida_class - Describes the different classes of gravida, such that primigravida means single pregnancy, secundigravida-second pregnancy, and tertigravida-third pregnancy</p> </li> <li> <p>Age - Describes the age of the participants recruited for the study</p> </li> <li> <p>HB_level - Describes the amount of hemoglobin in whole blood expressed in grams per deciliter (g/dl) during<br>enrolment</p> </li> <li> <p>Type of delivery - A spontaneous vaginal delivery (SVD) describes when a pregnant female goes into labor without the use of drugs or techniques to induce labor, and delivers her baby in the normal manner, without forceps, vacuum extraction, or a cesarean section (cs)</p> </li> <li> <p>N/A - Missing values for different variables</p> </li> </ul>
Improved library preparation protocols for amplicon sequencing-based noninvasive fetal genotyping for RHD-positive D antigen-negative alleles
<p>We aimed to simplify our fetal <i>RHD</i> genotyping protocol by changing the method to attach Illumina's sequencing adaptors to PCR products from the ligation-based method to a PCR-based method, and to improve its quantitative accuracy by introducing unique molecular indexes, which allow us to count the numbers of DNA fragments used as PCR templates and to minimize the effects of PCR and sequencing errors. Both of the newly established protocols reduced time and cost compared with our conventional protocol. Removal of PCR duplicates using UMIs reduced the frequencies of erroneously mapped sequences reads likely generated by PCR and sequencing errors. The modified protocols will help us facilitate implementing fetal <i>RHD</i> genotyping for East Asian populations into clinical practice.</p>
Parameter estimation and identifiability analysis for a bivalent analyte model of monoclonal antibody-antigen binding
<p>Data for non-regenerative bivalent analyte binding interaction between CH505 transmitted founder gp120 and CH31 monoclonal antibody, an HIV-1 mAb with CD4-binding site specificity.</p> <p>This data set is submitted as part of the manuscript titled "Parameter estimation and identifiability analysis for a bivalent analyte model of monoclonal antibody-antigen binding"</p>
Unique or not unique? Comparative genetic analysis of bacterial O-antigens from the Oxalobacteraceae family.Supplementary_data
<p>This is Supplementary files for the paper "Unique or not unique? Comparative genetic analysis of bacterial O-antigens from the Oxalobacteraceae family".</p> <p>The description for each dataset is located inside files.</p>
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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.