Single-cell adaptive immune receptor repertoire sequencing (scAIRR-seq) offers the possibility to access the nucleotide sequences of paired receptor chains from T-cell receptors (TCR) or B-cell receptors (BCR). Here we describe two protocols and the downstream bioinformatic approaches that facilitate the integrated analysis of paired T-cell receptor (TR) alpha/beta (TRA/TRB) AIRR-seq, RNA sequencing (RNAseq), immunophenotyping, and antigen-binding information. To illustrate the methodologies with a use case, we describe how to identify, characterize, and track SARS-CoV-2-specific T cells over multiple time points following infection with the virus. The first method allows the analysis of pools of memory CD8+ cells, identifying expansions and contractions of clones of interest. The second method allows the study of rare or antigen-specific cells and allows studying their changes over time.
CITATION STYLE
Gupta, N., Lindeman, I., Reinhardt, S., Mariotti-Ferrandiz, E., Mujangi-Ebeka, K., Martins-Taylor, K., & Eugster, A. (2022). Single-Cell Analysis and Tracking of Antigen-Specific T Cells: Integrating Paired Chain AIRR-Seq and Transcriptome Sequencing: A Method by the AIRR Community. In Methods in Molecular Biology (Vol. 2453, pp. 379–421). Humana Press Inc. https://doi.org/10.1007/978-1-0716-2115-8_20
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