Recent advances in single-cell sequencing allow for simultaneous profiling of T cell receptors (TCRs) and transcriptomes leading to the characterization of key T cell subsets with antigen recognition and killing capabilities. Despite their success, these methods rely on microfluidic devices or plate-based protocols with limited sensitivity and throughput (1,000s-10,000s of cells , 1-2 samples) making the study of disease-relevant T cells time consuming and costly.
To overcome these limitations, we developed a split pool combinatorial barcoding technology to simultaneously characterize the TCRs alongside the full transcriptomes of up to 1 million T cells from up to 96 unique samples. Here, we profiled over one million human T cells stimulated with tumor, viral, and autoantigens and included non-stimulated T cells from three donors as controls. Using our approach we recovered paired TCR clonotype information in 82% of all T cells. Moreover, we used the
top ten most expanded clonotypes in every sample, ran multiple sequence alignment and identified antigen-specific sequence motifs, some of which have been previously described.
In summary, we present a highly flexible and scalable combinatorial barcoding technology to allow researchers to profile up to 1 million T cells in a single experiment and investigate their functional responses during infection, cancer, autoimmunity, or therapeutic interventions.
