Love the idea of fixing the target antigen in a few (or a lot) of contexts, and watching thymocytes with variable TCR affinities develop down different routes. CITE-seq-esque tetramer reagents might work in this context, if they could quantitatively read out TCR affinity. The concern would probably be the abundance of tetramer-reactive cells in a polyclonal repertoire-- agree that perhaps if we fixed one chain and looked for enriched reactivities, that might get us somewhere. Would also be super cool to look at different types of antigens (self, viral, commensal, etc) and see if different trajectories become visible by scRNA-seq.

Definitely interesting to think about the range of states we'd want to survey. Is there any requirement that the profiling be unbiased, or could we enrich for rare states of interest? I like the idea of restricting the repertoire -- perhaps with a fixed Tcrb model?