DOI: 10.5061/dryad.wm37pvmvq
title: The TCR assigns naive T cells to a preferred lymph node

description: 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.
description: # 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. The bottom 5 rows describe technical replicates of specific samples (sequencing the same library again) and have a 'r' added to the sample code (also see column Comment). These are not used during the analysis; * The number of spike-in monoclonal (OT-II, DO11.10, or HA)-TCR transgene cells added to the sample; * Number of sorted cells and volume of Trizol added; * Sequencing set (L68 or L73) and sample pool (A-Z) that was used for grouped processing according to the input cell number; * Oligos used during PCRs: Template Switch Oligo (TSO) and reverse primer used during PCR-2 (full sequences of oligonucleotides provided in Table S3); * Number of PCR cycles for PCR-1 and PCR-2; * DNA concentration as quantified using NanoDrop and volume added to sample pool; * Comments describing problems with samples, indication of repeated sequencing (not used in analysis), or not applicable (n/a). Processed sequencing results are provided in *RTCR_output.zip*, which contains labelled the RTCR output for each sample described in the sample overview. The 'Number of reads' column refers to the number of unique UMIs that were accepted for a given TCRa sequence. The TCRa sequence is provided in therms of V gene, J gene, Junction sequence (amino acid and nucleotide). Scripts performing post-processing analyses on the sequencing data are provided in a Jupyter Notebook *oneTCRa_analysis.ipynb*.