Figure 5

Clonally expanded epitope-specific TCRs are identified in both RAPTER and a pooled oligo-tagged dextramer assays. PBMCs from an HLA-A*02:01⁺, A*29:02⁺, B*35:01⁺, and B*57:01⁺ healthy donor were expanded for 7 days with 22 HLA haplotyped matched and unmatched peptides (Supplementary Table 2) to expand epitope-specific T cells. (A) Schematic describing the RAPTER and pooled dextramer workflows that were performed on peptide-expanded T cells. Peptide-expanded T cells were divided and tested in either the RAPTER assay (0.5 × 10⁶ expanded PBMC assay per well; top panel) or a pooled oligo-tagged dCODE dextramer assay with 24 unique pooled dextramers (30 × 10⁶ expanded PBMC; bottom panel). (B) UMAP displaying CD8⁺ T cell clusters from the dCODE dextramer and RAPTER assays. (C) Correlation plots of paired TCR a/b chain sequence overlap between peptide expanded dextramer⁺ (y-axis) versus peptide expanded RAPTER⁺ (x-axis) CD8⁺ T cells across clone sizes (log10 scale). The dashed lines indicate TCR clone sizes >  = 5 cells.