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22 results for “antibody repertoire”
Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple spike epitopes
<p><strong>Abstract:</strong> Development of vaccines and therapeutics that are broadly effective against known and emergent coronaviruses is an urgent priority. We screened the circulating B cell repertoires of COVID-19 survivors and vaccinees to isolate over 9,000 SARS-CoV-2-specific monoclonal Abs (<strong>mAbs</strong>), providing an expansive view of the SARS-CoV-2-specific Ab repertoire. Among the recovered antibodies was TXG-0078, an NTD-specific neutralizing mAb that recognizes diverse alpha- and beta-coronaviruses. TXG-0078 achieves its exceptional binding breadth while utilizing the same VH1-24 variable gene signature and heavy chain-dominant binding pattern seen in other NTD supersite-specific neutralizing Abs with much narrower specificity. We also report the discovery of CC24.2, a pan-sarbecovirus neutralizing antibody that targets a novel RBD epitope and shows similar neutralization potency against all tested SARS-CoV-2 variants, including BQ.1.1 and XBB.1.5. A cocktail of TXG-0078 and CC24.2 protects <i>in vivo</i>, suggesting potential use in variant-resistant therapeutic Ab cocktails and as templates for pan-coronavirus vaccine design.</p><p><strong>Datasets: </strong>This repository contains the 10x Genomic cellranger outputs (matrix and vdj contig files) as well as complied functional characterization dataset used to generate figures on the publication "Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple spike epitopes". </p><p>Post-vaccination samples for donors CC10, CC25, CC31, CC66 were processed in single 10x Genomic reactions. The timepoints samples consist of multiplexing donors CC10, CC25, CC31, CC66 into one 10x Genomic reaction. Similarly, donors CC26, CC42, CC62, CC67 were multiplexed into a single 10x Genomic reaction.</p><p><strong>Files:</strong></p><p>feature names.csv - csv file with sort bait/antigen barcode key </p><p>feature_reference.csv - csv file with cell hash and antigen barcode reference</p><p>filtered_contig<i>_</i>annotations.csv - High-level annotations of each high-confidence contigs from cell-associated barcodes. This is a subset of all_contig_annotations.csv.</p><p>filtered_contig.fasta - filtered antibody fasta</p><p>filtered_matrix.mtx.gz - 10x Genomic matrix file for filtered cells. Contains counts data for feature and gene expression library.</p><p>raw_matrix.mtx.gz - 10x Genomic matrix file for unfiltered cells. Contains counts data for feature and gene expression library.</p><p><strong>Code: </strong>All code used to generate analysis and figures is available under the MIT license on Github<br> </p>
Simulated T-cells Rep-Seq datasets (called SIMTCR) from "Reconstructing antibody repertoires from error-prone immunosequencing datasets" paper
<p>Simulated test datasets used for benchmarking of immunorepertoire construction tools</p>
Simulated B-cells Rep-Seq datasets (called SIMULATED) from "Reconstructing antibody repertoires from error-prone immunosequencing datasets" paper
<p>Simulated test datasets used for benchmarking of immunorepertoire construction tools</p>
Imunnesenescence of antibody repertoire in individuals from endemic areas for infectious diseases
<p>Heavy Chain Antibody Repertoire data in the AIRR format, clonotyped with YClon, of patients diagnosed with COVID-19 and a control group. The sample labels in the paper and the sample labels in this repository are correspondent according to the following table:</p> <table> <tbody> <tr> <td>Sample</td> <td>Deposite_code</td> </tr> <tr> <td>C_01</td> <td>A04</td> </tr> <tr> <td>C_02</td> <td>A20</td> </tr> <tr> <td>C_03</td> <td>A24</td> </tr> <tr> <td>C_04</td> <td>A65</td> </tr> <tr> <td>C_05</td> <td>A66</td> </tr> <tr> <td>C_06</td> <td>A67</td> </tr> <tr> <td>H_NEA_01</td> <td>ID141</td> </tr> <tr> <td>H_NEA_02</td> <td>ID143</td> </tr> <tr> <td>H_NEA_03</td> <td>ID144</td> </tr> <tr> <td>H_NEA_04</td> <td>ID187</td> </tr> <tr> <td>H_NEA_05</td> <td>ID195</td> </tr> <tr> <td>H_NEA_06</td> <td>ID226</td> </tr> <tr> <td>H_NEA_07</td> <td>ID248</td> </tr> <tr> <td>H_NEA_08</td> <td>ID268</td> </tr> <tr> <td>H_NEA_09</td> <td>ID310</td> </tr> <tr> <td>H_NEA_10</td> <td>ID375</td> </tr> <tr> <td>M_EA_01</td> <td>GV43</td> </tr> <tr> <td>M_EA_02</td> <td>GV68</td> </tr> <tr> <td>M_EA_03</td> <td>GV106</td> </tr> <tr> <td>M_EA_04</td> <td>GV144</td> </tr> <tr> <td>M_EA_05</td> <td>GV146</td> </tr> <tr> <td>M_EA_06</td> <td>GV47</td> </tr> <tr> <td>M_EA_07</td> <td>GV50</td> </tr> <tr> <td>M_EA_08</td> <td>GV51</td> </tr> <tr> <td>M_EA_09</td> <td>GV54</td> </tr> <tr> <td>M_EA_10</td> <td>GV92</td> </tr> <tr> <td>M_NEA_01</td> <td>ID094</td> </tr> <tr> <td>M_NEA_02</td> <td>ID117</td> </tr> <tr> <td>M_NEA_03</td> <td>ID124</td> </tr> <tr> <td>M_NEA_04</td> <td>ID131</td> </tr> <tr> <td>M_NEA_05</td> <td>ID132</td> </tr> <tr> <td>M_NEA_06</td> <td>ID155</td> </tr> <tr> <td>M_NEA_07</td> <td>ID240</td> </tr> <tr> <td>M_NEA_08</td> <td>ID244</td> </tr> </tbody> </table>
Dynamics of heavy chain junctional length biases in antibody repertoires
Open the record for dataset details and reuse information.
Supplementary material 1 from: Pashova-Dimova S, Petrov P, Karachanak-Yankova S, Pashov A (2023) Neurodegenerative diseases associated antibody repertoire signatures in mimotope arrays based on cyclic versus linear peptides. Pharmacia 70(4): 1439-1447. https://doi.org/10.3897/pharmacia.70.e115179
Supplementary method
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.
Data from: A general approach for predicting protein epitopes targeted by antibody repertoires using whole proteomes
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Deep Characterization of the Human Antibody Response to Natural Infection Using Longitudinal Immune Repertoire Sequencing
GEO Series GSE123158. Homo sapiens. 210 samples. Type: Other.
Flexible chromatin loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire
GEO Series GSE43008. Mus musculus. 112 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing.
TCR repertoire and transcriptomic analyses of advanced solid tumors in first-in-human phase 1 study of IT1208, a defucosylated humanized anti-CD4 depleting antibody
GEO Series GSE120102. Homo sapiens. 124 samples. Type: Expression profiling by high throughput sequencing.
TCR repertoire analysis revealed the mobilization of novel CD8+ T cell clones into Cancer-Immunity Cycle following anti-CD4 antibody administration
GEO Series GSE115425. Mus musculus. 69 samples. Type: Other.
T-cell receptor repertoire analysis of advanced solid tumors in first-in-human phase 1 study of IT1208, a defucosylated humanized anti-CD4 depleting antibody [TCR-seq]
GEO Series GSE120101. Homo sapiens. 105 samples. Type: Expression profiling by high throughput sequencing.
Somatic hypermutation generates antibody specificities beyond the primary repertoire
GEO Series GSE283094. Mus musculus. 8 samples. Type: Other.
Public Baseline and Shared Response Structures Support the Theory of Antibody Repertoire Functional Commonality
<p>These four datasets accompany the original preprint "Evidence of Antibody Repertoire Functional Convergence through Public Baseline and Shared Response Structures", now revised to "Public Baseline and Shared Response Structures Support the Theory of Antibody Repertoire Functional Commonality".</p> <p>URL to preprint before revisions: https://www.biorxiv.org/content/10.1101/2020.03.17.993444v2.<br> <br> Included are both Antibody Model Libraries and two further files generated during peer-review.</p>
Combining mutation and recombination statistics to infer clonal families in antibody repertoires
<p>All data used for the benchmark of HILARy. The benchmark procedure is described here https://github.com/statbiophys/HILARy/tree/main/data_with_scripts </p>
IMPACT OF HUMAN IMMUNOGLOBULIN GENETIC VARIANTS ON THE EXPRESSED ANTIBODY REPERTOIRE
<p>Tables related to the PhD thesis of Eric Engelbrecht, mentored by Corey T. Watson</p>
Repertoire and Properties of Anti-drug Antibodies Involved in Immediate Hypersensitivity in the Operating Room
ClinicalTrials.gov study NCT05420935. IPD Sharing: NO. Countries: 1. Publications: 0.
Comprehensive Profiling of Rheumatoid Arthritis Antibody Repertoire
GEO Series GSE136052. Homo sapiens. 26 samples. Type: Protein profiling by protein array.
A Highly Sensitive and Unbiased Approach for Elucidating Antibody Repertoires
GEO Series GSE82126. Mus musculus. 57 samples. Type: Other.
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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.