Supplementary Materials

The PDF file includes:

  • Fig. S1. MASC type 1 error.
  • Fig. S2. t-SNE projection density.
  • Fig. S3. CIM analysis of clustering approaches.
  • Fig. S4. DensVM clustering of elbow plots.
  • Legend for fig. S5
  • Fig. S6. Association permutation testing and cluster alignment.
  • Fig. S7. PhenoGraph and FlowSOM clustering.
  • Fig. S8. Association testing with Citrus.
  • Fig. S9. Flow cytometry and RNA-seq gating strategies.
  • Fig. S10. CD27 and HLA-DR expression in flow cytometry cohort.
  • Fig. S11. CD4+ TEM populations in a clinical response cohort.
  • Fig. S12. CD27 HLA-DR+ frequency and clinical characteristics.
  • Fig. S13. RNA-seq analysis of CD4+ T cell subsets.
  • Fig. S14. Flow cytometry expression quantification.
  • Fig. S15. Using a neural network autoencoder to cluster mass cytometry data.
  • Table S1. Panel design for mass cytometry experiments.
  • Table S2. MASC analysis of the 19 clusters identified in the resting dataset.
  • Table S3. MASC analysis of the 21 clusters identified in the stimulated dataset.
  • Table S4. GSEA of genes differentially expressed in CD27 HLA-DR+ cells.

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Other Supplementary Material for this manuscript includes the following:

  • Fig. S5 (.pdf format). Marker expression distribution plots for DensVM clusters.