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52 results for “Immune repertoire”
Development of ferret immune repertoire reference resources and single-cell-based high- throughput profiling assays
<p>We performed long read transcriptome sequencing of ferret splenocyte and lymph node samples full-length, non-chimeric circular consensus sequencing (CCS) reads to obtain over 120,000 high-quality immunoglobin (Ig) and T cell receptor (TCR) transcripts.</p>
Immune repertoire profiling reveals that clonally expanded B and T cells infiltrating diseased human kidneys can also be tracked in the blood
<p>Recent advances in high-throughput sequencing allow for the competitive analysis of the human B and T cell immune repertoire. In this study we compared Immunoglobulin and T cell receptor repertoires of lymphocytes found in kidney and blood samples of 10 patients with various renal diseases based on next-generation sequencing data.</p>
Immune repertoire profiling reveals its clinical application potential and triggers for Neuromyelitis Optica Spectrum Disorders
<p>This dataset, containing TCRbeta-chain sequcening data of Neuromyelitis Optica Spectrum Disorders patients and healthy, is the basis for the following publication: "Immune repertoire profiling reveals its clinical application potential and triggers for Neuromyelitis Optica Spectrum Disorders".</p>
Immune repertoire sequencing reveals differences in treatment response to camrelizumab plus platinum-based chemotherapy in advanced ESCC
Open the record for dataset details and reuse information.
Single-cell immune repertoire sequencing of two convalescent COVID-19 patients
<p>Single-cell immune repertoire sequencing of two convalescent COVID-19 patients using 10x genomics 5' immune profiling. Resulting output files are from the count and vdj functions from 10x genomic's cellranger v3.1.0. </p>
Immune repertoires of de-identified TCGA tumor samples assembled by TRUST4
<p>We applied TRUST4 to assemble the immune repertoire data from TCGA tumor samples. Because TCGA has restricted access permission, the sample IDs are de-identified and the sequence is at the amino acid level. The data is used in the study of "Comprehensive characterizations of immune receptor repertoire in tumors and cancer immunotherapy studies". The format is:</p> <p>CancerType_RandomID Chain_Type CDR3_AminoAcid VGene JGene ConstantGene Abundance</p> <p>(Note that the deidentified RandomID is different from the previous version (version 1))</p>
Immune Gene Repertoire of Soft Scale Insects (Hemiptera: Coccidae)
<p>Dataset (fasta sequences and alignments) referred to the manuscript "<span>Immune Gene Repertoire of Soft Scale Insects (Hemiptera: Coccidae)"</span></p> <p><strong><span>Abstract: </span></strong><span>Insects possess an effective immune system which has been extensively characterized in several model species, revealing a plethora of conserved genes involved in recognition, signaling and response to pathogens and parasites. However, some taxonomic groups, characterized by peculiar trophic niches, such as plant-sap feeders, which are often important pests of crops and forestry ecosystems, have been largely overlooked regarding their immune gene repertoire. Here we annotated the immune genes of soft scale insects (Hemiptera: Coccidae), for which omics data are publicly available. By using immune genes of aphids and <em>Drosophila</em> to query the genome of <em>Ericerus pela</em>, as well as the transcriptomes of <em>Ceroplastes cirripediformis</em> and <em>Coccus</em> sp., we pointed out the lack of peptidoglycan recognition proteins, galectins, thaumatins and antimicrobial peptides in Coccidae</span><span>. This work contributes to expand our knowledge about the evolutionary trajectories of immune genes and offers a list of promising candidates for developing new control strategies based on the suppression of pests’ immunity through RNAi technologies.</span></p>
Benchmark datasets for "Detecting T-cell expansion and quantifying clone survival from deep profiling of immune repertoires"
<p>T-cell receptor repertoire sequencing datasets describing time courses obtained for vaccination, normal aging and blood transplant cases. Datasets reported here were previously published (except for Tem/Tcm data), this is just a compendium of selected samples that is properly pre-processed and formatted.</p>
Pilot Study in Young Adults to Examine the Kinetics of Changes in the B-cell Repertoire Following TIV Immunization
ClinicalTrials.gov study NCT02987374. IPD Sharing: YES. Countries: 0. Publications: 3.
A Prospective Study of Constructing Immune Repertoire to Monitor the Therapeutic Effect in NSCLC Patients
ClinicalTrials.gov study NCT03373955. IPD Sharing: UNDECIDED. Countries: 1. Publications: 11.
Investigation of the B- and T-cell Repertoire and Immune Response in Patients With Acute and Resolved COVID-19 Infection
ClinicalTrials.gov study NCT04362865. IPD Sharing: YES. Countries: 1. Publications: 3.
Single cell and immune repertoire profiling of COVID-19 patients reveal novel therapeutic candidates
<p>COVID-19, a novel pneumonia caused by SARS-CoV-2, has rapidly become the largest threat to public health. Recent studies reported lymphocytopenia but also expansions of antigen-specific T/B cells during early-recovery stage. Here we investigated 16 early-recovery patients using scRNA-seq, HLA-genotyping and deep immune repertoire profling. Our analysis revealed 916 COVID-19-specific TCR groups enriched for a novel cytotoxic CD8+ phenotype with both resident memory (ZNF683+) and tissue exit (SIRP5) markers, and identified 114 statistically-confident virus epitopes. Further, we uncovered 374 BCR groups with somatic hypermutations and/or class switch recombinations. Molecular dynamics simulations revealed 15% of the highly expanded groups may serve as neutralizing antibodies against the virus Spike protein. Finally, we discovered that bacterial infection in COVID-19 patients may elevate monocytic myeloidderived suppressor cells via TLR4/NF!B signaling and cause disease aggravation. Together, we expect our findings and immune-receptor datasets to provide immediate therapeutic options against the pandemic of COVID-19.</p>
Supplementary data for the manuscript, "Comprehensive Assessment of Physiochemical Metrics for the Clustering of Adaptive Immune Repertoires"
<p>This repository contains data and code used in the manuscript "Comparative Assessment of Physiochemical Metrics for the Clustering of Adaptive Immune Receptor Repertoires" by Girgis et al. For additional information regarding how these data were used, please refer to our manuscript.</p> <p>Code is organized per figure in the main text. Each figure folder contains a 'script-inputs' folder and 'script-outputs' folder. The outputs folder is empty and may be populated with graphs and results tables by executing code within the directory. The inputs folder contains some pre-formatted data which may be used in executing code. Most of these inputs may be generated from scratch using raw data (ie the results of Homolig clustering on simulated repertoires) but may require substantial time and/or computational resources. Raw patient data used in Figure 6 (Pancreatic cancer anti-mKRAS TCRB repertoire clustering) and Figure 7 (Rheumatoid arthritis TCRB and IGH repertoires) are not included here. However, several graphs may be reproduced stripped of sequence-specific data. Pancreatic cancer patient repertoire data will be made available on dbGaP,study accession number phs003425.v1.p1. Rheumatoid arthritis patient data will be made available on ImmuneAccess, accession pending.</p> <p>To browse repo, first unzip all subdirectories: </p> <blockquote> <p><code>for f in *.zip; do</code><br><code> unzip "$f"</code><br><code>done</code></p> </blockquote> <p>All non-code files have been compressed to .gz format. To decompress, use: <code>gzip -dr *</code>, or <code>pigz -dr ./raw-data/* </code>for parallel decompression (recommended). </p> <p>Alexander Girgis <br>agirgis3@jhmi.edu <br>July 2025 </p>
Immune repertoires for Bionumpy Blogpost
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Generation of Anti-HCV Antibodies From Bone Marrow: Defining the Repertoire of Immune Response to HCV Quasispecies
ClinicalTrials.gov study NCT00004851. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Adaptive Immune Responses and Repertoire in Influenza Vaccination and Infection (SLVP031)
ClinicalTrials.gov study NCT03028987. IPD Sharing: NO. Countries: 1. Publications: 0.
Seven chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
GEO Series GSE256256. Homo sapiens. 112 samples. Type: Other.
Deep Characterization of the Human Antibody Response to Natural Infection Using Longitudinal Immune Repertoire Sequencing
GEO Series GSE123158. Homo sapiens. 210 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.
Immune repertoire after immunization as seen by next generation sequencing and proteomics
GEO Series GSE98855. Rattus norvegicus. 10 samples. Type: Expression profiling by high throughput sequencing.
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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.