The αβTCR repertoire at scale in the immgenT dataset

The immensity of the T cell receptor (TCR) repertoire, shaped by combinatorial diversity, imprecise rearrangements, and clonal selection, makes it difficult to comprehend. The immgenT Project generated single-cell RNA and TCRseq to map paired {beta}TCR repertoires across 734 mouse T cell samples from diverse tissues, lineages and challenge conditions. Compositional analysis uncovered some extreme junctional architectures. Previously unreported recurrent recombinations suggested non-randomness in VDJ joining, broadening the precedent of quasi-invariant iNKT and MAIT TCRs. These, with public clonotypes linked to self or environmental factors, contribute to a highly skewed distribution of clonotype frequencies. Tissue analyses reveal compartmentalized and tissue-specific clonal expansions. Unproductive rearrangements of one V gene appeared to suppress the rearrangements of the same V gene on the second chromosome, suggesting that unproductive TCR transcripts may act as regulatory lncRNAs. This organism-wide look into the TCR repertoire offers novel insights on the evolutionary and immunological pressures on repertoire selection.