Identification of CD8⁺ bystander signature in the NHP model. (A) UMAP with Leiden clustering from NHP recipient R.315. Sixteen clusters are denoted by colors and labeled with inferred cell states. (B) UMAP with normalized CD8a and CD4 expression. (C) Heat map demonstrating normalized and log-scaled expression of selected T-cell activation, effector, and known bystander genes. (D) Cluster composition based on the time point of sample collection. (E) Differential expression of the bystander cluster (cluster 14) vs all other clusters in the data set. The top 6 upregulated (green) and downregulated (red) genes by median log2 fold change are labeled. (F) The 42 genes that exhibited upregulation in bystander signature 1 were classified based on their proposed function in T cells. (G) Heat map of Morisita index for all samples, comparing cluster 14 cells (at contraction and peak expansion) with all other cells using the clonotype ID inferred by Cell Ranger to group cells into clones.