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ShareScore release 0.9.0
Dataset results
65 results for “TCR sequencing”
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>
TIL1383I TCR mutation sequencing and SPR binding data
<p>Sequence and mutation sequence data for the TIL1383I TCR and surface plasmon resonance data and analysis files for TIL1383I binding to tyrosinase/HLA-A2.</p>
Datasets associated with the manuscript "Discovering SARS-CoV-2 neoepitopes and the associated TCR-pMHC recognition mechanisms by combining single-cell sequencing, deep learning, and molecular dynamics simulation techniques"
<p>meta_data_TCR-pMHC_from_STCRDab.tsv, TCR-pMHC structures used for contacts analysis.</p><p>tcr_gliph_input_sars2.tsv, input files (TCR sequences and related information) used for clustering TCRs targeting SARS-CoV-2 epitopes and epitope-unknown TCRs.</p><p>tcr_gliph_input_non-sars2.tsv, input files used for clustering TCRs targeting non-SARS-CoV-2 epitopes and epitope-unknown TCRs.</p><p>tcr_gliph_output*, output files from the GLIPH software, including the recognized TCR clusters by GLIPH (convergence-group.txt), the linkage information of TCR clusters (clone-network.txt), and the recognized motif in TCR clusters (kmer.txt).</p><p>md_trajs.tar, structures and MD simulation trajectories of TCR-614-pMHC and TCR-204-pMHC complexes.</p>
TCR repertoire sequencing related to "Unique roles of coreceptor-bound LCK in helper and cytotoxic T cells"
<p>This archive contains datasets needed for recapitulating the analysis of TCR repertoires for the manuscript <em>“Unique roles of coreceptor-bound LCK in helper and cytotoxic T cells”</em> by Horkova et al., 2022. The code for the analysis can be found on GitHub: https://github.com/Lab-of-Adaptive-Immunity/lck-tcrseq. Raw data are deposited in the SRA (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA872031).</p> <p>The Zenodo archive contains the following files, which are needed to run the analysis script:</p> <ul> <li>merged outputs from MiXCR <code>merged_TCR_repertoires.csv</code></li> <li>metadata file <code>metadata_Lck.csv</code></li> <li>TRA and TRB repertoires prepared for processing with the Immunarch package <code>immdata_tra.rds</code>, <code>immdata_trb.rds</code></li> </ul>
T Cell Receptor (TCR) Sequencing and Transcriptional Profiling in Adult Celiac Disease Patients Undergoing Gluten Challenge
ClinicalTrials.gov study NCT04614571. IPD Sharing: YES. Countries: 1. Publications: 0.
Murine TCR-beta repertoire sequencing
The purpose of this project was to determine the effects of chronic exposure to unpredictable mild socio-environmental stressors during gestation on the TCR-beta repertoire of newborn mice.
Single-cell transcriptome and TCR sequencing reveals immune cell heterogeneity in the submandibular gland of SS mice
GEO Series GSE253042. Mus musculus. 8 samples. Type: Other.
Novel TCR sequencing and cloning methods for sensitive and quantitative interrogation of repertoires and rapid isolation of tumor-reactive TCRs
GEO Series GSE225984. Homo sapiens; Mus musculus. 34 samples. Type: Other.
TCR sequencing of Treg and Tconv subsets from murine spleen
GEO Series GSE121147. Mus musculus. 24 samples. Type: Expression profiling by high throughput sequencing.
Single-cell TCR-sequencing of T cells in crescentic glomerulonephritis
GEO Series GSE223107. Mus musculus; Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing; Other.
Single-cell RNA-sequencing combined with TCR-sequencing of GP66+ splenic CD4+ T cells on day 10 post LCMV Cl13 infection
GEO Series GSE201730. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing; Other.
Single cell RNA sequencing and TCR repertoire analysis of MIS-C affected patients versus healthy controls and severe adult COVID-19
GEO Series GSE184330. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
TCR beta sequencing in LMP2-positive and LMP2-negative human T cells treated with anti-PD-L1 and anti-TIM3 antibodies.
GEO Series GSE182537. Homo sapiens. 31 samples. Type: Other.
High-throughput Ig and TCR repertoire single-cell sequencing analysis in rhesus macaques
GEO Series GSE179722. Macaca mulatta. 5 samples. Type: Expression profiling by high throughput sequencing.
Single Cell Immunophenotyping of Lyme Erythema Migrans (Bulk TCR Repertoire Sequencing)
GEO Series GSE172225. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Single-cell transcriptional profiling identifies a spectrum of unconventional intraepithelial T lineage cells in human cord blood [TCR sequencing]
GEO Series GSE201810. Homo sapiens. 16 samples. Type: Other.
Single-Cell Analysis of Transcriptome and TCR Sequencing Reveals Immune Cell Atlas and Functional Heterogeneity of T Cell Repertoire in Murine Heart Transplantation
GEO Series GSE249989. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
TCR sequencing analysis of islets from NOD mice on hydrolyzed casein and hydrolyzed casein + 4% gluten diets
GEO Series GSE218336. Mus musculus. 24 samples. Type: Expression profiling by high throughput sequencing; Other.
Single-cell TCR sequencing of in vitro peripheral blood cell stimulation in ankylosing spondylitis
GEO Series GSE207037. Homo sapiens. 1 samples. Type: Other.
Single-Cell RNA Sequencing of Thymic KN6 γδ T-Cells Modulated by TCR Signal Strength and Notch Signaling
GEO Series GSE165908. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
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DANDI Archive for NWB datasets
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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.