Science Immunology

The PDF file includes:

  • Fig. S1. Supplementary figures for mutation analysis.
  • Fig. S2. Controls and additional DSF assay results.
  • Fig. S3. Supplementary figures for PBMC analysis.
  • Fig. S4. Supplementary figures for scRNA-seq analysis.
  • Fig. S5. Quality control plots for scRNA-seq analysis and outlier clusters.
  • Table S1. Wild type epitopes investigated in this study.
  • Table S3. Peptides used in the study and their % rank predicted by netMHCpan v4.1.
  • Table S4. Tm values for peptides tested in DSF assay.
  • Table S5. Characteristics of HLA-A*02:01/HLA-B*40:01 positive patients.
  • Table S6. HLA genotypes.
  • Table S7. Overview of ELISpot results for wild type peptides.

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Other Supplementary Material for this manuscript includes the following:

  • Table S2. Samples with epitope mutations at allele frequency >0.02 (Excel spreadsheet).
  • Table S8. DEGs from scRNA-seq analysis (Excel spreadsheet).
  • Table S9. Top clonotypes from TCR sequencing (Excel spreadsheet).
  • Table S10. Acknowledgments for sequences downloaded from GISAID (separate PDF file).
  • Table S11. Raw data (Excel spreadsheet).
  • Reproducibility checklist.