Figure 2
Re-clustering of T cells. (a) The UMAP plot illustrates the four equine BALF T cell groups. The expression of three top differentially expressed markers is mapped onto the UMAP plot, which is shown to the right. (b) The proportion of T cell subtypes in the EA vs healthy group of horses is depicted. (c) The differential expression of T cell cluster markers visualized with a heat map. (d) Iterative clustering reveals seven subpopulations of CD4+ cells. The subset coloured in brown in the heat map (T-ISGHi) expresses interferon stimulated genes, and the yellow subset (T-S100Hi) displays higher expression of S100 genes and other genes involved in cytoskeleton organization and cell adhesion, as indicated by GO analysis. The heat map shows the genes with the highest fold changes in the T-ISGHi and T-S100Hi relative to the other clusters. The green label indicates data from the horses sampled at the clinic and the blue label indicates data from the research herd. (e) Iterative clustering of the CD8+TR cluster shows eight subclusters. The brown subset (T-ISGHi) selectively expresses interferon stimulated genes. The heat map shows the genes with the highest fold changes in the T-ISGHi cluster relative to the other clusters. See Supplementary Fig. S3 and Supplementary Table S3 for the proportions of case and control cells within the clusters.
