Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

5c638551-978c-4e80-b87e-d669d6b7069e - samples

ABSTRACT: Full information about the T cell receptor (CR) variable regions found in the sequences of the vdj region. Columns: barcode is_cell contig_id high_confidence length chain v_gene d_gene j_gene c_gene full_length productive cdr3 cdr3_nt reads umis raw_clonotype_id raw_consensus_id

PROVIDER: EGAD00001008109 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Publications

SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8+ T cell responses.

Agerer Benedikt B Koblischke Maximilian M Gudipati Venugopal V Montaño-Gutierrez Luis Fernando LF Smyth Mark M Popa Alexandra A Genger Jakob-Wendelin JW Endler Lukas L Florian David M DM Mühlgrabner Vanessa V Graninger Marianne M Aberle Stephan W SW Husa Anna-Maria AM Shaw Lisa Ellen LE Lercher Alexander A Gattinger Pia P Torralba-Gombau Ricard R Trapin Doris D Penz Thomas T Barreca Daniele D Fae Ingrid I Wenda Sabine S Traugott Marianna M Walder Gernot G Pickl Winfried F WF Thiel Volker V Allerberger Franz F Stockinger Hannes H Puchhammer-Stöckl Elisabeth E Weninger Wolfgang W Fischer Gottfried G Hoepler Wolfgang W Pawelka Erich E Zoufaly Alexander A Valenta Rudolf R Bock Christoph C Paster Wolfgang W Geyeregger René R Farlik Matthias M Halbritter Florian F Huppa Johannes B JB Aberle Judith H JH Bergthaler Andreas A

Science immunology 20210301 57

CD8+ T cell immunity to SARS-CoV-2 has been implicated in COVID-19 severity and virus control. Here, we identified nonsynonymous mutations in MHC-I-restricted CD8+ T cell epitopes after deep sequencing of 747 SARS-CoV-2 virus isolates. Mutant peptides exhibited diminished or abrogated MHC-I binding in a cell-free in vitro assay. Reduced MHC-I binding of mutant peptides was associated with decreased proliferation, IFN-γ production and cytotoxic activity of CD8+ T ...[more]

PMID: 33664060

Similar Datasets

Full-length single-cell BCR sequencing paired with RNA sequencing reveals convergent responses to vaccination

Project description:Single-cell RNA sequencing can resolve transcriptional features from individual cells, but techniques capable of resolving the variable regions of B cell receptors (BCRs) – defining features that confer antigen specificity to B cells – remain limited, especially from widely-used 3`-barcoded libraries. Here, we report a method that can recover paired, full-length variable region sequences of BCRs from 3`-barcoded single-cell whole transcriptome libraries. We applied this method to produce accurate, full-length BCR sequences from cDNA of human PBMC generated following the 10x Genomics 3`GEX protocol.

2024-07-07 | GSE266697 | GEO

Analysis of IGH repertoire in MRL/lpr SLE prone mice treated with either control SMO or Long isoform of PRLR SMO

Project description:Purpose: IGH sequencing has revolutionized analysis of structural and functional signatures of B cell clonality. The goals of this study are to compare IGH repertoire of splenic B cells before and after knockdown of long isoform of PRLR. Methods: After amplifying the IGH repertoire of splenic B cells using PCR primers for VHJ558 variable and Cμ constant regions. For next generation sequencing (NGS), a TrueSeq library was prepared by adapter ligation to full-length products and sequenced on the MiSeq Illumina 2x150 bp platform. Results: In this project, Unique nucleotide sequences were identified, their abundances were calculated, and their complementary determining region 3 (CDR3) length, CDR3 spectrum, VDJ usage, and diversity were analyzed using the International Immunogenetics Information System (IMGT) HighV-QUEST software. Controls are included C3,C4,C5,C7,C8 and C9. LFPRLR SMO treated mice samples are: A3,A4,A5,A6,A7 and A8

2023-03-06 | GSE207186 | GEO

Unbiased quantification of immunoglobulin diversity at the DNA level with VDJ-seq

Project description:For high-throughput sequencing and quantification of immunoglobulin repertoires, most methodologies utilise RNA. However, output varies enormously between recombined genes due to different promoter strengths and differential activation of lymphocyte subsets, precluding quantitation of recombinants on a per cell basis. To date, DNA-based approaches have used V gene primer cocktails, with substantial inherent biases. Here we describe VDJ-seq, which accurately quantitates immunoglobulin diversity at the DNA level in an unbiased manner. This is accomplished with a single primer extension step using biotinylated J gene primers. By addition of unique molecular identifiers (UMI) before primer extension, we reliably remove duplicate sequences and correct for sequencing and PCR errors. Furthermore, VDJ-seq captures productive and non-productive VDJ and DJ recombination events on a per cell basis. Library preparation takes 3 days, with 2 days of sequencing, and 1 day of data processing and analysis.

2017-12-16 | GSE106458 | GEO

PRJEB60070

Project description:HLA-A full length sequences

| PRJEB60298 | ENA

Full-length HLA class II sequences

Project description:Full-length HLA class II sequences

| PRJEB42469 | ENA

Project description:full-length transcriptome sequences of ginkgo

| PRJNA485059 | ENA

Human immunodeficiency virus 1

Project description:Full-length HIV-1 envelope sequences

| PRJNA320111 | ENA

scRNA-seq of mESC and mouse CD4+ cells using different buffers and enzymes

Project description:Existing protocols for full-length single-cell RNA sequencing (scRNA-seq) produce libraries of high complexity (thousands of distinct genes) with outstanding sensitivity and specificity of transcript quantification. These full-length libraries have the advantage of allowing probing of transcript isoforms, are informative regarding single nucleotide polymorphisms, and allow assembly of the VDJ region of the T- and B-cell receptor sequences. Since full length protocols are mostly plate-based at present, they are also suited to profiling cell types where cell numbers are limiting, such as rare cell types during development for instance. A disadvantage of these methods has been the scalability and cost of the experiments, which has limited their popularity as compared to droplet-based and nanowell approaches. Here, we describe an automated protocol for full-length scRNA-seq, including both an in-house automated SMART-seq2 protocol, and a commercial kit-based workflow. We discuss these two protocols in terms of ease-of-use, equipment requirements, running time, cost per sample and sequencing quality. By benchmarking the lysis buffers, reverse transcription enzymes and their combinations, we propose an optimized in-house automated protocol with dramatically reduced cost. These pipelines have been employed successfully for several research projects allied with the Human Cell Atlas initiative (www.humancellatlas.org) and are available on protocols.io.

2020-12-31 | E-MTAB-9345 | biostudies-arrayexpress

Ablation of SetD2 impaired the lymphocyte development in mouse models.

Project description:The repertoire of diverse T-cell receptors (TCRs) and immunoglobulins is generated through restrictedly lineage and stage specific DNA rearrangements of variable (V), diversity (D) and Joining (J) gene segments at early T and B cell development. Histone modifications has been demonstrated to ensure proper VDJ recombination. However, the epigenetic mechanisms and the role of enzymes that catalyze epigenetic modifications in regulating VDJ recombination still remain largely unexplored. Herein we report that deletion of SetD2, the histone methyltransferase to catalyze the trimethylation of lysine 36 on histone 3, leads to severe lymphopenia due to development blockage of T lymphocyte at the double negative 3 (DN3) stage and differentiation arrest of B cell development at the pro-B stage in genetically engineered mouse models. SetD2 deficiency causes a loss of H3K36me3 and markedly impairs VDJ rearrangement of TCRβ and immunoglobulin heavy chain. Our study demonstrates that SetD2 and its mediated H3K36M3 modification are required for the VDJ recombination and normal lymphocyte development.

2019-02-01 | GSE116685 | GEO

BASIC: B-cell receptor (BCR) assembly from single cell RNA-seq

Project description:The B-cell receptor (BCR) enables individual B cells to identify diverse antigens, including bacterial and viral proteins. While advances in RNA-seq have enabled high throughput profiling of transcript expression in single cells, the unique task of assembling the full-length heavy and light chain sequences from single cell RNA-sequencing (scRNA-seq) in B cells has been largely unstudied. We developed a new software tool, BASIC, which allows investigators to use scRNA-seq for assembling BCR sequences at single cell level. To demonstrate the utility of our software, we subjected single B cells from a human donor to scRNA-seq, assembled the full-length heavy and the light chains, and experimentally confirmed these results by using single cell primer based nested PCRs and Sanger sequencing.

2016-06-02 | E-MTAB-4745 | biostudies-arrayexpress