Abstract
High-throughput antibody repertoire analysis via next-generation sequencing is a key method in understanding humoral immunity. Errors introduced during library preparation and sequencing can be corrected with molecular amplification fingerprinting using unique molecular identifiers. Here, we provide a step-by-step protocol for laboratory and bioinformatic workflows to perform sequencing in murine cells with isotype-specific primers, obtaining total and isotype-specific B cell receptor repertoires. This enables the examination of isotype-dependent immune responses and improves the understanding of underlying mechanisms in humoral immunity. For complete details on the use and execution of this protocol, please refer to Khan et al. (2016).