The TCR assigns naive T cells to a preferred lymph node

Naive T cells recirculate between the spleen and lymph nodes where they mount immune responses when meeting dendritic cells presenting foreign antigen. As this may happen anywhere, naive T cells ought to visit all lymph nodes. Here, deep sequencing almost-complete TCR-repertoires led to a comparison of different lymph nodes within and between individual mice. We find strong evidence for a deterministic CD4/CD8 lineage choice and a consistent spatial structure. Specifically, some T cells show a preference for one or multiple lymph nodes, suggesting that their TCR interacts with locally presented (self-)peptides. These findings are mirrored in TCR-transgenic mice showing localized CD69-expression, retention, and cell division. Thus, naïve T cells intermittently sense antigenically dissimilar niches, which is expected to affect their homeostatic competition., , , # The TCR assigns naive T cells to a preferred lymph node

[https://doi.org/10.5061/dryad.wm37pvmvq](https://doi.org/10.5061/dryad.wm37pvmvq)

## Description of the data and file structure

This dataset contains TCRa sequencing data from oneTCRa mice as described in de Greef *et al.*, SciAdv 2024. See the Methods section for the full description of the experimental and computational procedures. The 199 samples that were sequenced are described in the *oneTCRa_sample_overview.csv* file. The information in this overview includes:

* Cell content of samples. Samples are labeled with a 4-character code:  1) A letter corresponding to a mouse pool (I, J, L control mice; D, F CD62L-treated mice; H pool of CD62L-treated mice); 2) A letter corresponding to the sorted cell population (A CD4 Tconv; B CD4 Treg; C CD8); 3) A letter corresponding to the specific lymph node (see Fig. 1A); 4) A number being 1 normally, or 2 if the sample contained too many cells to be processed in a single sample.
Th...