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The TCR assigns naive T cells to a preferred lymph node

Cite this dataset

de Greef, Peter et al. (2024). The TCR assigns naive T cells to a preferred lymph node [Dataset]. Dryad. https://doi.org/10.5061/dryad.wm37pvmvq

Abstract

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.

README: The TCR assigns naive T cells to a preferred lymph node

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.

Funding

Deutsche Forschungsgemeinschaft, Award: FOR1961 Ki611/2-1

Deutsche Forschungsgemeinschaft, Award: Ki611/2-2

Dutch Research Council, Award: 022.005.023