Any plans to incorporate thymocytes -- T cells, but mostly not yet of the functional variety -- into the profiling? Will special provisions be needed to really understand the VDJ information in this context, given the changes in the pre- to post-selection repertoires?
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For thymocytes, is definitely on to run balanced sampling, otherwise data will be overwhelmed by pretty boring DPs. What is currently on the books is to rebalance by over-sampling double-negatives and intermediate/mature TCRhi cells. But there are probably sharper ways to rebalance (especially for the gdT side of things)
And yes, having some relation to TCR strength-of-signal would definitely be desirable. Not sure that a single-chain TCR transgenic would give us that handle (variability in the second chain would likely create a wide range of affinities for thymic MHC-peptide complexes). But selection by tetramer staining (that one perhaps coupled with a single-chain Tg), or focusing on super-antigen reactive T cells, might get us there.
Thanks, Dan! Yes, profiling thymocytes is undoubtedly within the project's scope, i.e., especially analyzing the types of T cells and states that emerge during differentiation. Thymus-specific states that don't make it to the periphery would be equally interesting. TCR repertoire is a tricky one considering its size. The technology isn't powered to answer broad repertoire analysis. Maybe we could consider experimental models with a limited range or models testing different T cell paths?