High‐throughput single‐cell sequencing of paired TCRα and TCRβ genes for the direct expression‐cloning and functional analysis of murine T‐cell receptors

Precise clonal and functional assessments of the T cell receptor (TCR) repertoire diversity require paired TCRα and TCRβ gene sequence information at monoclonal level. However, available single‐cell strategies are typically limited in throughput and often do not provide full‐length DNA templates for direct gene cloning. Here, we describe a high‐throughput strategy for the unbiased amplification and automated sequence analysis of paired TCRα and TCRβ genes from primary mouse T cells. The platform links cell phenotype and TCR gene sequence information at single‐cell level. Furthermore, it enables direct functional analyses through the efficient cloning of both genes and the generation of stable TCR expressing cell lines. This highly efficient workflow is a powerful tool to determine the diversity and quality of the murine T‐cell repertoire in various settings, for example in vaccine development, infectious diseases, autoimmunity, or cancer.