Fig. 5

DN T cells constitute an unconventional subset of T cells in the FRT with a distinct gene expression profile. A Diagram of experimental procedures. B Identification of CD3 + DN T cells via oligo-conjugated antibody expression. C Analysis of protein expression, RNA expression or protein + RNA integrated data plotted in Uniform manifold approximation and projection (UMAP) graphs from T cell subsets: CD4 + (blue), CD8 + (yellow), DN (purple) and double positive T cells (grey). D Venn diagram shows genes expressed in DN T cells, CD4 + and CD8 + T cells. E Volcano plot showing differentially expressed genes comparing DN vs CD4 + T cells (left panel) and DN vs CD8 + T cells (right panel) (significance p ≤ 0.05; -2 < Fold Change > 2). F Hierarchical clustering heatmaps comparing relative expression levels of surface markers (AbSeq) and (G) analogous RNA expression. H Percentage of each T cell population expressing tissue-resident related profiles: CD103 oligo-conjugated antibody, and transcripts for CD69, S1PR1 and CCR7. I Heat map of selected CD molecules, transcription factors and secreted proteins differentially expressed in DN, CD4 + and CD8 + T cells. (Significance p ≤ 0.05; -1.2 < Fold Change > 1.2). J Bubble plot shows the enriched gene ontology (GO) terms significantly upregulated in DN T cells vs CD4 + or DN T cells vs CD8 + , that are associated to functions related to cytotoxicity, regulation, antigen presentation and innate immunity. K Bubble plot shows enriched KEGG pathways in DN T cells vs CD4 + and DN T cells vs CD8 + T cells