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1,973 results for “T cell receptor”
Data from: Consistency of VDJ rearrangement and substitution parameters enables accurate B cell receptor sequence annotation
VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D, or J genes, or from an N-addition (a.k.a. non-templated insertion). Previous work has used simple parametric distributions to model transitions from state to state in a hidden Markov model (HMM) of VDJ recombination, and assumed that mutations occur via the same process across sites. However, codon frame and other effects have been observed to violate these parametric assumptions for such coding sequences, suggesting that a non-parametric approach to modeling the recombination process could be useful. In our paper, we find that indeed large modern data sets suggest a model using parameter-rich per-allele categorical distributions for HMM transition probabilities and per-allele-per-position mutation probabilities, and that using such a model for inference leads to significantly improved results. We present an accurate and efficient BCR sequence annotation software package using a novel HMM "factorization" strategy. This package, called partis (https://github.com/psathyrella/partis/), is built on a new general-purpose HMM compiler that can perform efficient inference given a simple text description of an HMM.
Pre-processed B-cell receptor amplicon sequencing data from SRR1842411
<p>An example dataset containing B-cell receptor (BCR) gene sequences. This dataset is intended to be used for testing software tools developed to annotate (i.e. map Variable, Diversity and Joining segments) and perform clonal analysis of BCR sequencing data.</p> <p><strong>Sequencing:</strong></p> <p>Libraries prepared using 5'RACE from PBMCs of a healthy donor. Input molecules were tagged with unique molecular identifiers (UMIs). Sequencing was ran on MiSeq , 300+300bp reads.</p> <p><strong>Contents:</strong></p> <p>The dataset contains both raw sequencing reads and high-quality consensus sequences assembled using unique molecular tagging (UMI) approach. Consensus assembly corrects for sequencing errors and eliminates sequencing artifacts.</p> <ul> <li>age_ig_s7_R1.fastq.gz and age_ig_s7_R2.fastq.gz contain raw reads</li> <li>age_ig_s7_R1.t10.cf.fastq.gz and age_ig_s7_R2.t10.cf.fastq.gz contain consensus sequences</li> </ul> <p>All files contain an UMI tag sequence in their header, in form UMI:NNNN:QQQQ where N is the base character and Q is the quality character (for assembled consensuses the total number of reads is given instead of Q string).</p> <p>Note that consensus sequences were assembled using only raw sequences that correspond to UMI tags supported by at least 10 sequencing reads. That means that consensus sequence files contain a subset of all UMI tags found in raw sequences. Thus, if one wants to assess software performance on raw sequencing reads using assembled consensus sequences as a high-quality data standard, raw sequencing reads should be filtered to contain only those UMI tags that are present in consensus sequence file.</p> <p><strong>Citations:</strong></p> <p>The whole dataset was used to benchmark MiXCR software and was originally referenced in Bolotin DA, et al. MiXCR: software for comprehensive adaptive immunity profiling Nature methods 12(5):380-381, 2015.</p> <p>Data pre-processing was carried out using MIGEC software, Shugay M et al. Towards error-free profiling of immune repertoires. Nature Methods 11(6):653-655, 2014.</p> <p><strong>Contributors:</strong></p> <p>The dataset was generated in Prof. Chudakov lab (Adaptive Immunity Group in Masaryk University, Brno and Genomics of Adaptive Immunity Lab in Institute of Bioorganic Chemistry, Moscow). Sample preparation and sequencing was performed by Dr. Olga Britanova and Dr. Maria Turchaninova. Raw sequencing reads were pre-processed and uploaded by Dr. Mikhail Shugay.</p>
Pep-TCRNet: Prediction of Multi-Class Peptides by T-cell Receptor Sequences with Deep Learning
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Tumor control via targeting PD-L1 with chimeric antigen receptor modified NK cells
<p>Failed T cell-based immunotherapies in the presence of genomic alterations in antigen presentations pathways may be overcome by NK cell-based immunotherapy. This approach may still be limited by the presence of immunosuppressive myeloid populations. Here we demonstrate that NK cells (haNKs) engineered to express a PD-L1 chimeric antigen receptor (CAR) haNKs killed a panel of human and murine head and neck cancer cells at low effector-to-target ratios in a PD-L1-dependent fashion. Treatment of syngeneic tumors resulted in CD8 and PD-L1-dependent tumor rejection or growth inhibition and a reduction in myeloid cells endogenously expressing high levels of PD-L1. Treatment of xenograft tumors resulted in PD-L1 dependent tumor growth inhibition. PD-L1 CAR haNKs reduced levels of macrophages and other myeloid cells endogenously expressing high PD-L1 in peripheral blood from patients with head and neck cancer. The clinical study of PD-L1 CAR haNKs is warranted.</p>
Benchmarking tree and ancestral sequence inference for B cell receptor sequences
<p>Simulation data used and described in associated article.</p>
Genomic analysis of T cell receptors in a cohort of Lynch Syndrome carriers distinguishes pre-malignant and malignant status
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Data from: Respiratory virus infection up-regulates TRPV1, TRPA1 and ASICS3 receptors on airway cells
Receptors implicated in cough hypersensitivity are transient receptor potential vanilloid 1 (TRPV1), transient receptor potential cation channel, Subfamily A, Member 1 (TRPA1) and acid sensing ion channel receptor 3 (ASIC3). Respiratory viruses, such as respiratory syncytial virus (RSV) and measles virus (MV) may interact directly and/or indirectly with these receptors on sensory nerves and epithelial cells in the airways. We used in vitro models of sensory neurones (SHSY5Y or differentiated IMR-32 cells) and human bronchial epithelium (BEAS-2B cells) as well as primary human bronchial epithelial cells (PBEC) to study the effect of MV and RSV infection on receptor expression. Receptor mRNA and protein levels were examined by qPCR and flow cytometry, respectively, following infection or treatment with UV inactivated virus, virus-induced soluble factors or pelleted virus. Concentrations of a range of cytokines in resultant BEAS-2B and PBEC supernatants were determined by ELISA. Up-regulation of TRPV1, TRPA1 and ASICS3 expression occurred by 12 hours post-infection in each cell type. This was independent of replicating virus, within the same cell, as virus-induced soluble factors alone were sufficient to increase channel expression. IL-8 and IL-6 increased in infected cell supernatants. Antibodies against these factors inhibited TRP receptor up-regulation. Capsazepine treatment inhibited virus induced up-regulation of TRPV1 indicating that these receptors are targets for treating virus-induced cough.
Data from: Enhanced B-cell receptor recognition of the autoantigen transglutaminase 2 by efficient catalytic self-multimerization
A hallmark of the gluten-driven enteropathy celiac disease is autoantibody production towards the enzyme transglutaminase 2 (TG2) that catalyzes the formation of covalent protein-protein cross-links. Activation of TG2-specific B cells likely involves gluten-specific CD4 T cells as production of the antibodies is dependent on disease-associated HLA-DQ allotypes and dietary intake of gluten. IgA plasma cells producing TG2 antibodies with few mutations are abundant in the celiac gut lesion. These plasma cells and serum antibodies to TG2 drop rapidly after initiation of a gluten-free diet, suggestive of extrafollicular responses or germinal center reactions of short duration. High antigen avidity is known to promote such responses, and is also important for breakage of self-tolerance. We here inquired whether TG2 avidity could be a feature relevant to celiac disease. Using recombinant enzyme we show by dynamic light scattering and gel electrophoresis that TG2 efficiently utilizes itself as a substrate due to conformation-dependent homotypic association, which involves the C-terminal domains of the enzyme. This leads to the formation of covalently linked TG2 multimers. The presence of exogenous substrate such as gluten peptide does not inhibit TG2 self-cross-linking, but rather results in formation of TG2-TG2-gluten complexes. The celiac disease autoantibody epitopes, clustered in the N-terminal part of TG2, are conserved in the TG2-multimers as determined by mass spectrometry and immunoprecipitation analysis. TG2 multimers are superior to TG2 monomer in activating A20 B cells transduced with TG2-specific B-cell receptor, and uptake of TG2-TG2-gluten multimers leads to efficient activation of gluten-specific T cells. Efficient catalytic self-multimerization of TG2 and generation of multivalent TG2 antigen decorated with gluten peptides suggest a mechanism by which self-reactive B cells are activated to give abundant numbers of plasma cells in celiac disease. Importantly, high avidity of the antigen could explain why TG2-specific plasma cells show signs of an extrafollicular generation pathway.
Localisation of oestrogen receptors in stem cells and in stem cell derived neurons of the mouse
<p>This dataset is linked to a publication in the Journal of Neuroendocrinology with the following DOI: 10.1111/jne.13220</p> <p>The Readme file gives details of the organisation of this dataset. All data here are raw data obtained from image analyses using the EZcoloc plugin for Fiji (Image J) and this raw data was used to construct the data graphs that are shown in the paper. In some graphs that involve ratios, integrated density values from Fiji were used.</p> <p>The softwares used are EZcoloc plugin and Image J referenced in the Readme file.</p>
Administering Peripheral Blood Lymphocytes Transduced With a Murine T-Cell Receptor Recognizing Human Thyroglobulin to People With Thyroglobulin Expressing Thyroid Cancer
ClinicalTrials.gov study NCT02390739. IPD Sharing: Not stated. Countries: 0. Publications: 3.
Study of GSK3359609 and Pembrolizumab in Programmed Death Receptor 1-ligand 1 (PD-L1) Positive Recurrent or Metastatic Head and Neck Squamous Cell Carcinoma
ClinicalTrials.gov study NCT04128696. IPD Sharing: YES. Countries: 26. Publications: 0.
A Study of ASP2215 in Combination With Erlotinib in Subjects With Epidermal Growth Factor Receptor (EGFR) Activating Mutation-Positive (EGFRm+) Advanced Non-Small-Cell Lung Cancer (NSCLC) Who Have Acq
ClinicalTrials.gov study NCT02495233. IPD Sharing: NO. Countries: 1. Publications: 0.
Aumolertinib With Chemotherapy or Alone Compared With Osimertinib in Patients With Epidermal Growth Factor Receptor-Mutant Non-Small Cell Lung Cancer
ClinicalTrials.gov study NCT05493501. IPD Sharing: Not stated. Countries: 1. Publications: 0.
The Molecular Epidemiology of Epidermal Growth Factor Receptor (EGFR) Mutations in Patients With Advanced EGFR Mutation-positive Non-small Cell Lung Cancer Treated With Afatinib
ClinicalTrials.gov study NCT04640870. IPD Sharing: NO. Countries: 0. Publications: 24.
The Role of Neutrophil CD64 and Soluble Triggering Receptor Expressed on Myeloid Cells 1 in Neonatal Sepsis
ClinicalTrials.gov study NCT03795285. IPD Sharing: Not stated. Countries: 0. Publications: 4.
A Study of RO4929097 in Patients With Advanced Renal Cell Carcinoma That Have Failed Vascular Endothelial Growth Factor (VEGF)/Vascular Endothelial Growth Factor Receptor (VEGFR) Therapy
ClinicalTrials.gov study NCT01141569. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Xentuzumab (BI 836845) Plus Afatinib in Patients With Epidermal Growth Factor Receptor (EGFR) Mutant Non-small Cell Lung Cancer (NSCLC)
ClinicalTrials.gov study NCT02191891. IPD Sharing: YES. Countries: 4. Publications: 0.
T Cell Cytokine Changes During IL-4 Receptor Treatment for Asthma
ClinicalTrials.gov study NCT00001908. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Upfront Chimeric Antigen Receptor T-Cell to Upgrade Response in Multiple Myeloma
ClinicalTrials.gov study NCT05032820. IPD Sharing: YES. Countries: 1. Publications: 0.
Development and Validation of in Vitro Cell-based Bioassays for Nuclear Receptor Activation
ClinicalTrials.gov study NCT02434562. IPD Sharing: Not stated. Countries: 0. Publications: 1.
ScienceDex guides
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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.