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2,285 results for “T-cells”
Spectral decompositions dataset for the paper "Random walk informed heterogeneities detection reveals how the lymph node conduits network influences T-cells collective exploration behavior"
<p>This file contains the left and right approximated eigenvectors, as well as the approximated eigenvalues of the networks analyzed in the paper : Random walk informed heterogeneities detection reveals how<br> the lymph node conduits network influences T-cells collective<br> exploration behavior</p>
KSR inhibitor APS-2-79 sensitivity test in JURKAT and ALL-SIL T-cell acute lymphoblastic leukemia cell lines measured by Cell Counting Kit 8
<p>APS-2-79 compound was purchased from MedChemExpress (Monmoutyh Junction, NJ, USA). The 20 mg/ml stock solution was prepared in DMSO. To calculate the IC50, JURKAT and ALL-SIL cells were cultured for 72h with a range of APS-2-79 concentrations (5-15 µM) added as equal volumes. Cells treated with 0.5% DMSO (vehicle) were used as negative control. Cells treated with 10% DMSO were used as positive control. The viability of cells was measured using Cell Counting Kit 8 (Sigma Aldrich) and GloMax Microplate Reader system (Promega) with 450 nm wavelength and 600 nm as reference wavelength. The relevant reads are made from following wells: 2A-2D (15 µM APS-2-79), 3A-3D (12.5 µM APS-2-79), 4A-4D (10 µM APS-2-79), 5A-5D (7.5 µM APS-2-79), 6A-6D (5 µM APS-2-79), 7A-7D (vehicle), 8A-8D (positive control).</p>
In vivo treatment with insulin-like growth factor 1 reduces CCR5 expression on vaccine-induced activated CD4+ T-cells
<p>Dataset of the publication "In vivo treatment with insulin-like growth factor 1 reduces CCR5 expression on vaccine-induced activated CD4+ T-cells" by Bissa et al. on the journal Vaccines. </p><p>Each folder contains the original files reporting the data used to generate the manuscript.</p><p>For flowcytometry based assays the Flow panel is included in the folders. </p><p>For ELISA based assays the schemes of the plates are included in the folders. </p><p>The excel table "Bissa et al._Vaccines_2023_Animal IDs and viral acquisition" reports the IDs and grouping of the animals together with their viral acquisition</p><p>The excel table "Bissa et al._Vaccines_2023_Master table" reports each data used to generate the figures and supplemental materials included in the publication </p>
Control T-cell receptor (TCR) alpha and beta chain nucleotide and amino acid sequences from human and mouse
<p>A dataset of pooled T-cell receptor (TCR) sequences for TCR alpha and beta chains of human and mouse.</p> <p>Sequences are obtained from various samples of healthy individuals/mice using our conventional protocols: see for example [Britanova et al "Dynamics of individual T cell repertoires: from cord blood to centenarians" The Journal of Immunology 2016] and [Izraelson et al. "Comparative analysis of murine T‐cell receptor repertoires." Immunology 2018].</p> <p>The sequences are stored as gzipped clonotype tables in VDJtools format, see [https://vdjtools-doc.readthedocs.io/en/master/input.html#vdjtools-format].</p> <p>This control dataset can be used as a proxy for a generative VDJ rearrangement model to estimate the expected frequency distribution of TCRs and check for enrichment of rare TCR clonotypes and groups of similar TCR sequences. For the implementation of the enrichment analysis, please see CalcDegreeStats routine from VDJtools software, see [https://vdjtools-doc.readthedocs.io/en/master/annotate.html#calcdegreestats].</p> <p>Files named "human.tra.strict.txt.gz", etc are pools of random/naive TCR clonotypes containing unique V/J/CDR3 nucleotide sequence combinations observed in data. The pools.zip file is used for TCR motif inference in VDJdb database [https://github.com/antigenomics/vdjdb-motifs], it contains human.tra.aa.txt, etc files that contain random/naive TCR clonotypes grouped by CDR3 amino acid sequence with the most frequent representative V and J.</p>
Computationally profiling peptide:MHC recognition by T-cell receptors and T-cell receptor-mimetic antibodies
<p>Supporting datasets for preprint version of "Computationally profiling peptide:MHC recognition by T-cell receptors and T-cell receptor-mimetic antibodies".</p>
Fig. 3 in SjTat-TPI facilitates adaptive T-cell responses and reduces hepatic pathology during Schistosoma japonicum infection in BALB/c mice
Fig. 3 Th1 immune response acter CD8+T cells blockage in sitro. a. CD3+CD8+T cells were successcullv blocked. The blocking ecciciencv was more than 99.6 %. b, c. Percentages oc CD4+IFN-γ+ (Th1) in Tat-TPI (T-TPI), TPI stimulated splenocvtes with or without CD8+T-cell blockage. Data are presented as the means ± SEM crom cour independent experiments. (*P <0.05; **P <0.01)
Fig. 2 in SjTat-TPI facilitates adaptive T-cell responses and reduces hepatic pathology during Schistosoma japonicum infection in BALB/c mice
Fig. 2 Immune responses in the draining popliteal lvmph nodes oc mice induced bv Tat-TPI (T-TPI) and TPI proteins. a and c. Percentages oc CD4+IFN-γ+ cells (Th1), CD8+IFN-γ+ cells (Tc1) analvsed bv FACS. b. The ratio oc CD4+ T cells to CD8+ T cells (CD4/CD8) in the draining popliteal lvmph nodes. Data are presented as the means ± SEM crom six mice in each group. (*P <0.05; **P <0.01)
Fig. 1 in SjTat-TPI facilitates adaptive T-cell responses and reduces hepatic pathology during Schistosoma japonicum infection in BALB/c mice
Fig. 1 Expression, puricication and identicication oc the cusion proteins Tat-TPI and TPI. a. Puricication oc two cusion proteins detected bv Protein Gel Electrophoresis. M: molecular weight marker, Lane 1: recombinant SjTat-TPI, Lane 2: recombinant SjTPI, Lane 3: the recombinant plasmid without puricication. b. Fusion proteins recognised bv His-Ab with Western blotting. Lane 1: recombinant SjTat-TPI, Lane 2: recombinant SjTPI. c. Fusion proteins recognised bv S. japonicum incected-mice serum with Western blotting. Lane 1: recombinant SjTat-TPI, Lane 2: recombinant SjTPI
Fig. 5 in SjTat-TPI facilitates adaptive T-cell responses and reduces hepatic pathology during Schistosoma japonicum infection in BALB/c mice
Fig. 5 Parasite burden and immune response were obsersed at 6 weeks acter S. japonicum incection in mice saccinated with T-TPI + IFA, TPI + IFA, IFA and PBS. a. Aserage number oc worms recosered. b. Aserage number oc eggs per gram (EPG) in the liser. c. Representatise granulomas with a single egg crom each group (100×). d. Aserage area oc single egg granulomas crom each group. e, f. Percentages oc CD3+CD4+IFN-γ+(Th1) and CD3+CD8+IFN-γ+(Tc1) gated crom CD3+ T cells analvsed bv FACS. Each bar represents the means ± SEM crom twelse mice per group. (*P <0.05; **P <0.01)
Fig. 4 T cell and antibodies responses acter three immunisations with T in SjTat-TPI facilitates adaptive T-cell responses and reduces hepatic pathology during Schistosoma japonicum infection in BALB/c mice
Fig. 4 T cell and antibodies responses acter three immunisations with T-TPI + IFA, TPI + IFA, IFA and PBS. a and b: Percentages oc CD3+CD4+IFN-γ+ (Th1) and CD3+CD8+IFN-γ+ (Tc1) gated crom CD3+ cells analvsed bv FACS. c. IgG, IgG1 and IgG2a lesels in mice sera were detected. Data are presented as the means ± SEM crom eight mice in each group. (*P <0.05; **P <0.01)
Single cell T-cell Atlas (V3)
<p>The attached datasets comprised of the merging of 21 high quality single cell T cell based dataset that had both the TCR-seq and GEx. The object contains ~1.3 paired TCR-seq with GEx in the Seurat Object (<a target="_blank" rel="noopener noreferrer">supercluster_added_ID-240531.rds</a>).</p> <p>We also included the original identifiers in the <a target="_blank" rel="noopener noreferrer">Sup_Update_labels.csv</a> a. See our <a href="https://stegor.readthedocs.io/en/latest/" target="_blank" rel="noopener">https://stegor.readthedocs.io/en/latest/</a> for how we processed the 12 datasets (V2) and decided on the current 47 T cell annotation models using scGate (TcellFunction). Additionally, based on collaborator recommendataion, we have also now included a simpler T cell annotion model in STEGO.R process (Tsimplefunctions). </p> <p>This is the accompanying data set for the paper entitled ‘T cell receptor-centric approach to streamline multimodal single-cell data analysis.’, which is currently available as a preprint (<a href="https://www.biorxiv.org/content/10.1101/2023.09.27.559702v2" target="_blank" rel="noopener">https://www.biorxiv.org/content/10.1101/2023.09.27.559702v2</a>). Details on the origin of the datasets, and processing steps can be found there.</p> <p>The purpose of this atlas both the full dataset and down sampling version is to aid in improving the interpretability of other T cell based datasets. This can be done by adding in the down sampled object that contains up to 500 cells per annotation model. This dataset aims to improve the capacity to identify TCR-specific signature by ensuring a well covered background, which will improve the robustness of the FindMarker Function in Seurat package.</p> <p> </p>
MAGE-A3-specific T-cells
<p>Single-cell RNA-seq data of MAGE-A3-specific T-cells genereated with the BD Rhapsody™ system.</p> <p>Donor information: 3 healthy subjects, 2 male (SampleTag01, SampleTag03), 1 female (SampleTag02).</p> <p>Cell preparation: MAGE-A3-specific T-cells were obtained via a Tetramer-based sorting of the naturally-occuring anti-CD3 and anti-CD28-activated T-cells co-cultured with the Dendritic cells that were maturated by a KVAELVHFL peptide. </p> <p>Single-cell analysis system: BD Rhapsody™</p> <p>Library strategy: 5' mRNA sequencing</p> <p>Library preparation protocol: BD Rhapsody™ TCR/BCR Full Length, Targeted mRNA, and Sample Tag Library Preparation</p> <p>mRNA panel: BD Rhapsody™ Immune Response Panel HS</p> <p>BD Pipeline version: 1.12</p>
Altered T-cell Reactivity to β-amyloid-related Antigens in Early Alzheimer's Disease
<p>The code generated during this study is available at this online repository with free access. Further information and requests for resources should be directed to and will be fulfilled by the Lead Contact, Dr. Christoph Gericke (christoph.gericke@irem.uzh.ch).</p>
Celluloepidemiology: a novel paradigm for quantifying infectious disease dynamics through T-cell modelling on a population level
<p>T-cell receptor sequencing (TCR-seq) was performed on enriched CD8+ T-cells. TCR clonotype annotation was performed using MiXCR v.3.0.13 with the default input parameters.</p> <p>Full origin and method description available in:<br>Celluloepidemiology: a novel paradigm for quantifying infectious disease dynamics through T-cell modelling on a population level</p>
Peripheral T-cell profiling reveals downregulated exhaustion marker and increased diversity in lymphedema post-lymphatic venous anastomosis
<p>In this study, we compared T cell receptor (TCR) repertoire diversity between patients with lymphedema, post-lymphatic venous anastomosis and healthy controls (HCs). TCR diversity was decreased in lymphedema compared with HCs; such TCR skewing was drastically improved in post-LVA.</p>
CyTOF and Flow Cytometry dataset assocaited with "Early-to-mid stage idiopathic Parkinson's disease shows enhanced cytotoxicity and differentiation in CD8 T-cells in females"
<p>This dataset contains all the raw mass cytometry (CyTOF) and flow cytometry fcs files associated with Capelle <i>et al</i>. '<i>Early-to-mid stage idiopathic Parkinson's disease shows enhanced cytotoxicity and differentiation in CD8 T-cells in females',</i> <i><strong>Nature Communications</strong>, <strong>2023</strong>,</i> In Press.</p><p>The dataset contains the following information:</p><p>1, The folder " CoPImmunoPD Flow Zenodo V2.zip " contains all the raw fcs files of flow cytometry analysis and the excel table with marker information of five staining panels in the initial discovery analysis using fresh blood samples. The folder also includes the fcs files of analyzing cytotoxicity potential within CD8 T cells and of validation analyses using cryopreserved samples. Single-color/fluorochrome staining files have also been provided for the relevant experiments in the given subfolders for compensation.</p><p>2, The folder "<a href="https://zenodo.org/api/files/75c910aa-3615-4eff-a201-9d2d46e33ea0/CoPImmunoPD_CyTOF_Zenodo.zip">CoPImmunoPD_CyTOF_Zenodo.zip</a>" contains all the raw fcs files generated from the CyTOF measurements in the initial discovery analysis.</p><p><strong>To reproduce our published Figures, please be assure to first read all the accompanied readme/excel information annotation files deposited in the corresponding folders within the zip files, all the Source Data files of different main and supplementary Figure subpanels, Methods and/or any other relevant sections in our manuscript.</strong></p>
A Phase 3 Trial of Brentuximab Vedotin(SGN-35) Versus Physician's Choice (Methotrexate or Bexarotene) in Participants With CD30-Positive Cutaneous T-Cell Lymphoma (ALCANZA Study)
ClinicalTrials.gov study NCT01578499. IPD Sharing: YES. Countries: 12. Publications: 5.
Valemetostat Tosylate (DS-3201b), an Enhancer of Zeste Homolog (EZH) 1/2 Dual Inhibitor, for Relapsed/Refractory Peripheral T-Cell Lymphoma (VALENTINE-PTCL01)
ClinicalTrials.gov study NCT04703192. IPD Sharing: YES. Countries: 12. Publications: 1.
T-SCAPE: T-cell immunogenicity scoring via cross-domain aided predictive engine
Open the record for dataset details and reuse information.
Co-exposure of uranyl acetate and sodium arsenite differentially alters gene expression in CD3/CD28 activated CD4+ T-cells.
Communities in the western region of the United States experience environmental exposure to metal mixtures from living in proximity to numerous unremediated abandoned uranium mines. Metals including arsenic and uranium co-occur in and around these sites at levels higher than the United States Environmental Protection Agency maximum contaminant levels. To address the potential effect of these metals on the activation of CD4+ T-cells, we used RNA sequencing methods to determine the effect of exposure to uranyl acetate, sodium arsenite or a mixture of uranyl acetate and sodium arsenite. Oxidative stress is a mechanism proposed for metal toxicity, but findings for uranium differ across cell models. No significant changes in oxidative stress genes were detected for uranyl acetate, in contrast to sodium arsenite. Sodium arsenite induced a dose dependent effect on activation associated gene expression, targeting immune response genes at the lower dose. While uranyl acetate alone did not significantly alter activation associated gene expression, the mixture demonstrated a combined effect relative to sodium arsenite alone. The results demonstrate the need to investigate uranium alone and in metalloid mixtures at environmentally relevant concentrations to better understand the toxicological impact of these mixtures on T-cell activation, function and immune dysregulation.
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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.