The αβTCR repertoire at scale in the immgenT dataset

Croze, M.; Yang, L.; Candeias, S.; Magill, I.; Casey, O.; Piekarsa, V.; Vijaykumar, B.; Giudicelli, V.; Kossida, S.; Zemmour, D.; Benoist, C.; Project, i.

doi:10.64898/2026.01.30.702900

bioRxiv · 10.64898/2026.01.30.702900

The αβTCR repertoire at scale in the immgenT dataset

Croze, M.·Yang, L.·Candeias, S.·Magill, I.·Casey, O.·Piekarsa, V.·Vijaykumar, B.·Giudicelli, V.·Kossida, S.·Zemmour, D.·Benoist, C.·Project, i.

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Abstract

The immense T cell receptor (TCR) repertoire is shaped by VDJ combinatorial diversity, imprecise rearrangements, and clonal selection. The immgenT Project generated scRNA and TCRseq to map paired {beta}TCR repertoires across 734 mouse samples from diverse tissues and challenge conditions. Compositional analysis uncovered some extreme junctional architectures. Beyond probabilistic V and J pairing, over-represented joins suggested non-randomness in fine joining, broadening the precedent of quasi-invariant iNKT and MAIT TCRs. We charted public clonotypes linked to self or environmental antigens in the main lineages. Tissue analyses revealed compartmentalized tissue-specific expansions. Unproductive and productive rearrangements of a V gene appeared to interfere specifically with each other, at chromatin or RNA levels. Unexpectedly, allelic exclusion at TCR{beta} proved less stringent than thought, and we identified rearrangements of TCR in immature pre-T stages. This organism-wide look into the TCR repertoire offers novel insights on the evolutionary and immunological pressures on TCR repertoire selection.

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Croze, M., Yang, L., Candeias, S., Magill, I., Casey, O., Piekarsa, V., Vijaykumar, B., Giudicelli, V., Kossida, S., Zemmour, D., Benoist, C., Project, i.. 2026-02-02. The αβTCR repertoire at scale in the immgenT dataset. https://doi.org/10.64898/2026.01.30.702900

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