Science Immunology

Supplementary Materials

Supplementary Material for:

Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis

Veena S. Patil, Ariel Madrigal, Benjamin J. Schmiedel, James Clarke, Patrick O?Rourke, Aruna D. de Silva, Eva Harris, Bjoern Peters, Gregory Seumois, Daniela Weiskopf, Alessandro Sette, Pandurangan Vijayanand*

*Corresponding author. Email: vijay{at}lji.org

Published 19 January 2018, Sci. Immunol. 3, eaan8664 (2017)
DOI: 10.1126/sciimmunol.aan8664

This PDF file includes:

  • Materials and Methods
  • Fig. S1. Most of the expanded TCR clonotypes are DENV-specific.
  • Fig. S2. TEMRA cells cluster into four distinct clusters.
  • Fig. S3. Batch analysis of TEMRA cells.
  • Fig. S4. TEMRA clusters express distinct set of transcripts.
  • Fig. S5. Clusters 1 and 2 are enriched for transcripts involved in cytotoxicity-related pathways.
  • Fig. S6. Precursor cells in TEMRA subset.
  • Fig. S7. CD4-CTL precursors share clonotypes with CD4-CTL effectors.
  • Fig. S8. Smart-seq2 is more sensitive compared with droplet-based approach (10× genomics).
  • Table S1. Summary of study donors.
  • Table S3. Summary of TCRα and TCRβ chains recovered from full-length single-cell transcriptomes of all single cells in the 15 donors.
  • Table S10. List of antibodies used in the study.
  • Table S11. Primers used for TCR-seq.
  • References (64—73)

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Other Supplementary Material for this manuscript includes the following:

  • Table S2 (Microsoft Excel format). List of differentially expressed genes between memory subsets for data in Fig. 1 (B and C).
  • Table S4 (Microsoft Excel format). TCRα and TCRβ chain reconstruction from full-length single-cell transcriptome of every single cell sequenced from the 15 donors.
  • Table S5 (Microsoft Excel format). List of differentially expressed genes between clusters (for data in Fig. 4C and fig. S4).
  • Table S6 (Microsoft Excel format). List of differentially expressed genes between TCM and CD4-CTL effectors (for data in Fig. 5H).
  • Table S7 (Microsoft Excel format). TCRα and TCRβ chain sequences derived from TCR-seq analysis of 14 donors for data in Fig. 6 (E and F) and fig. S7.
  • Table S8 (Microsoft Excel format). TCRα and TCRβ chain clonotype sharing derived from TCR-seq analysis of longitudinally collected samples from five donors (for data in Fig. 6F and fig. S7).
  • Table S9 (Microsoft Excel format). List of differentially expressed genes between the two clusters in donors #1 and #2 for data in Fig. 7 (A and B).
  • Table S12 (Microsoft Excel format). List of gene sets used for GSEA (for data in Fig. 1E).
  • Source data (Microsoft Excel format)

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