TCR-sequencing of KSHV-specific T cell clones

In this study, we sequenced the T cell receptor of previously isolated T cell clones specific for KSHV LANA (Sabbah et al., doi: 10.1182/blood-2011-07-36). T cell clones were thawed and cultured in vitro for several weeks. RNA was isolated directly after thawing the T cell clones in week 0. RNA was further isolated upon two or four weeks of culture. The TCR alpha and TCR Beta chains from all samples were sequenced using an open-source TCR-library preparation and computation analysis pipeline described by the Chain lab at UCL London (Oakes et al., doi: 10.3389/fimmu.2017.01267). For sequencing, the prepared libraries were processed on an Illumina MiSeq platform with a paired end reads configuration of 201-8-8-101. The Decombinator software v4.2 available on Github (https://github.com/innate2adaptive/Decombinator) was used to analyze the sequencing results.