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Lio britton code#
All original code has been deposited at Zenodo and is publicly available as of the date of publication. The code for Morisita-Horn similarity heatmaps, tree-maps and circos plots was produced with R packages.
Lio britton software#
The code for TCR sequence alignment derived from version 3.0.13 of the MiXCR software ( Bolotin et al., 2013) and from version 1.2.9 of the MIGEC software ( Shugay et al., 2014). Microscopy data reported in this paper will be shared by the lead contact upon request. Accession numbers are listed in the key resources table.
Single-cell RNA-seq data have been deposited at GEO and are publicly available as of the date of publication.
TCR sequencing data generated for this study are available at and are publicly available as of the date of publication. We speculate that dominant proinflammatory T cell clones might provide a therapeutic target in human inflammatory bowel disease. Our results demonstrate key aspects of intestinal CD4 + T cell activation and suggest that few microbial species exert a dominant effect on the intestinal T cell repertoire during colitis. Identical TCRα clonotypes accumulated in the colon of different individuals, whereas antibiotics or defined colonization correlated with the expansion of distinct expanded T cell clonotypes. We show that dominant TCRα clonotypes were shared between interferon-γ- and interleukin-17-producing but not regulatory Foxp3 + T cells. Here we tracked adoptively transferred T cell populations to specify the interrelation of T cell receptor repertoire and the gut antigenic environment. Key aspects of intestinal T cells, including their antigen specificity and their selection by the microbiota and other intestinal antigens, as well as the contribution of individual T cell clones to regulatory and effector functions, remain unresolved.
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