Takara Bio, San Jose, CA, USA.
Department of Immunology, Oslo University Hospital and K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.
Methods Mol Biol. 2022;2453:379-421. doi: 10.1007/978-1-0716-2115-8_20.
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.
单细胞适应性免疫受体库测序（scAIRR-seq）提供了从 T 细胞受体（TCR）或 B 细胞受体（BCR）获取配对受体链核苷酸序列的可能性。在这里，我们描述了两种方案和下游生物信息学方法，这些方法有助于整合分析配对 T 细胞受体（TR）α/β（TRA/TRB）AIRR-seq、RNA 测序（RNAseq）、免疫表型和抗原结合信息。为了通过一个用例来说明这些方法，我们描述了如何在感染病毒后多个时间点识别、表征和跟踪 SARS-CoV-2 特异性 T 细胞。第一种方法允许分析记忆 CD8 细胞的池，鉴定感兴趣的克隆的扩增和收缩。第二种方法允许研究稀有或抗原特异性细胞，并允许随时间研究它们的变化。
