Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High-Throughput and High-Dimensional Single Cell Analysis of Antigen-Specific CD8+ T cells

ABSTRACT: High-Throughput and High-Dimensional Single Cell Analysis of Antigen-Specific CD8+ T cells

PROVIDER: PRJNA732729 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Clinical study on diagnosis of colorectal cancer based on high-throughput tumor antigen polypeptides screening

Project description:Interventions: Gold Standard:Pathological diagnosis;Index test:high-throughput tumor antigen polypeptides screening Primary outcome(s): Diagnostic accuracy Study Design: Factorial

| 2704426 | ecrin-mdr-crc

Clinical study on individualized and precise immunotherapy for colorectal cancer based on high-throughput tumor antigen polypeptides screening

Project description:Interventions: therapy group:Individualized and precise immunotherapy for colorectal cancer based on high-throughput tumor antigen polypeptides screening Primary outcome(s): Incidence of adverse events;Progression free survival Study Design: Single arm

| 2705817 | ecrin-mdr-crc

Optimizing High-Throughput Shotgun Immunoproteomics for Antigen Identification

Project description:Identification of individual proteins (i.e., antigens) which initiate and/or perpetuate adaptive immune responses has potential to greatly impact pre-clinical and clinical work across numerous fields. To date, however, the methodologies available to identify antigens responsible for driving adaptive immune responses have been plagued by numerous issues which have drastically limited their widespread adoption. Therefore, in this study, we sought to optimize a shotgun immunoproteomics approach to alleviate these persistent issues and create a high-throughput, quantitative methodology for antigen identification. Three individual components of a previously published approach, namely the protein extraction, antigen elution, and LC-MS/MS analysis steps, were optimized in a systematic manner. These studies determined that preparation of protein extracts using a one-step tissue disruption method in immunoprecipitation (IP) buffer, eluting antigens from affinity chromatography columns with 1% trifluoroacetic acid (TFA), and TMT-labeling & multiplexing equal volumes of eluted samples for LC-MS/MS analysis, resulted in quantitative longitudinal antigen identification, with reduced variability between replicates and increased total number of antigens identified. This optimized pipeline provides a multiplexed, highly reproducible, and fully quantitative approach to antigen identification which is broadly applicable to determine the role of antigenic proteins in inciting (i.e. primary antigens) and perpetuating (i.e., secondary antigens) a wide range of diseases.

2023-04-18 | PXD038761 | Pride

CD8+ T cell gene expression after different antigen dose stimulations

Project description:This study aimed to identify the human T cell response toward different antigen doses. Fresh isolated CD8+ T cells from peripheral blood mononuclear cells (PBMCs) were stimulated with influenza M1 peptide-loaded autologous monocyte-derived dendritic cells for 2 weeks. A high M1 peptide antigen dose (10uM on moDC, HD1-5) and an optimal antigen dose (10nM on moDC OD1-5) were used. M1-specific CD8 T cells were tetramer sorted at the end of the 2 weeks. RNA was extracted and analyzed for gene expression using Agilent 8X60K gene expression microarrays. 5 independent samples from 3 different HLA A2+ blood donors.

2013-12-01 | E-GEOD-39761 | biostudies-arrayexpress

High-throughput profiling of antigen-specific antibody secreting cells using an antibody secretion trap (TRAPnSeq)

Project description:Following activation by cognate antigen, B cells undergo fine-tuning of their antigen receptors and may ultimately differentiate into antibody-secreting cells (ASCs). While antigen-specific antibodies from B cell receptor (BCR) expressing B cells can be readily cloned and sequenced following flow sorting, antigen-specific plasma cells that lack surface BCR cannot be easily profiled in a high-throughput way. Here, we report an approach, TRAPnSeq (antigen specificity mapping through Ig secretionTRAPandSequencing), that allows capture of secreted antibodies on the surface of ASCs, which in turn enables high-throughput screening of single ASCs against large antigen panels and recovery of paired VH:VL antibody sequences. This approach incorporates flow cytometry, standard microfluidic platforms and DNA barcoding technologies to isolate and characterize antigen-specific ASCs through single cell V(D)J, RNA and antigen barcode sequencing. We show the utility of TRAPnSeq by profiling antigen-specific IgG and IgE plasma cells from mouse and humans and validate antigen binding by ELISA. TRAPnSeq can easily be combined with existing B cell platforms to accelerate antibody discovery from ASCs and can further be expanded to any protein secreting-cells.

2023-07-07 | GSE233507 | GEO

Pd-1 High and Intermediate CD8+ T cells

Project description:During acute viral infections, naïve CD8+ T cells differentiate into effector CD8+ T cells and, after viral control, into memory CD8+ T cells. Memory CD8+ T cells are highly functional, proliferate rapidly upon reinfection and persist long-term without antigen. In contrast, during chronic infections, CD8+ T cells become “exhausted” and have poor effector function, express multiple inhibitory receptors, possess low proliferative capacity, and cannot persist without antigen. Exhuasted CD8+ T cells can be further segregated by their expression of the inhibitory cell surface receptor PD-1. We performed transcriptional profiling on both PD-1 High and PD-1 Intermediate H2-Db GP33-specific CD8+ T cells. H2-Db GP33-specific CD8+ T cells were sorted from C57BL/6 mice 30 days p.i. with LCMV clone 13. These cells were then segregated by their expression of the inhibitory cell surface receptor PD-1 into PD-1 High and PD-1 Intermediate subpopulations. We performed transcriptional profiling on these subpopulations.

2014-10-24 | E-GEOD-41869 | biostudies-arrayexpress

Transcriptomics coupled proteomics reveals the critical signaling pathways regulating OVA antigen-specific CD8+ T cells in mouse spleen and liver

Project description:Antigen-specific T cells are particularly important for eliminating bacterial infection, and the dynamics in this process help uncover the mechanisms by which bacteria are eliminated.This study used MHC class I tetramers to recognize the antigen OVA antigen-specific CD8+ T cells in mouse spleen and liver. Then combined the RNAseq and LC-MS/MS analysis to track the changes of the OVA antigen-specific CD8+ T cells at different time points (5 days,7 days, and 14 days post listeria infection).Transcriptomics coupled proteomics reveals the key signaling pathways to regulate antigen-specific CD8+ T cells by infection of Listeria monocytogenes expressing the OVA protein in mouse spleen and liver.

2024-03-26 | PXD050970 | iProX

CD8+ T cell gene expression after different antigen dose stimulations

2013-12-01 | GSE39761 | GEO

High-throughput determination of the antigen specificities of T cell receptors in single cells

Project description:High-throughput determination of the antigen specificities of T cell receptors in single cells

| PRJNA488855 | ENA

High-throughput determination of the antigen specificities of T cell receptors in single cells

Project description:High-throughput determination of the antigen specificities of T cell receptors in single cells

| PRJNA488856 | ENA