Supplementary Materials

The PDF file includes:

  • Materials and Methods
  • Fig. S1. Gating strategies for cells isolated by fluorescence-activated cell sorting.
  • Fig. S2. Architecture of the codes used for our k-mer profiling workflow.
  • Fig. S3. TSA validation process.
  • Fig. S4. MS validation of CT26 and EL4 TSA candidates using synthetic analogs.
  • Fig. S5. Detection of antigen-specific CD8+ T cells in naïve and immunized mice.
  • Fig. S6. Frequencies of antigen-specific T cells.
  • Fig. S7. Correlation between antigen-specific T cell frequencies in naïve and immunized mice.
  • Fig. S8. Purity of the 10H080 B-ALL sample after expansion in NSG mice.
  • Fig. S9. Overview of the human TEC and mTEC transcriptomic landscapes.
  • Fig. S10. MS validation of B-ALL TSA candidates using synthetic analogs.
  • Fig. S11. MS validation of lung cancer TSA candidates using synthetic analogs.
  • References (6068)

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Other Supplementary Material for this manuscript includes the following:

  • Table S1. Statistics related to the generation of the global cancer databases.
  • Table S2. Information about samples used in this study.
  • Table S3. List of CT26 MHC class I–associated peptides.
  • Table S4. List of EL4 MHC class I–associated peptides.
  • Table S5. Accession numbers of the ENCODE datasets used in this study.
  • Table S6. Features of murine TSAs.
  • Table S7. Experimental values obtained in analyses of mouse TSA immunogenicity.
  • Table S8. List of 07H103 MHC class I–associated peptides.
  • Table S9. List of 10H080 MHC class I–associated peptides obtained by mild acid elution.
  • Table S10. List of 10H080 MHC class I–associated peptides obtained by immunoprecipitation.
  • Table S11. List of 10H118 MHC class I–associated peptides.
  • Table S12. List of 12H018 MHC class I–associated peptides.
  • Table S13. List of lc2 MHC class I–associated peptides.
  • Table S14. List of lc4 MHC class I–associated peptides.
  • Table S15. List of lc6 MHC class I–associated peptides.
  • Table S16. Accession numbers of the Genotype-Tissue Expression (GTEx) datasets used in this study.
  • Table S17. Features of human TSAs detected in B-ALL specimens.
  • Table S18. Features of human TSAs detected in lung tumor biopsies.