Supplementary Material for:

Functional inflammatory profiles distinguish myelin-reactive T cells from patients with multiple sclerosis

Yonghao Cao, Brittany A. Goods, Khadir Raddassi, Gerald T. Nepom, William W. Kwok, J. Christopher Love, David A. Hafler*

*Corresponding author. E-mail: david.hafler{at}yale.edu

Published 13 May 2015, Sci. Transl. Med. 7, 287ra74 (2015)
DOI: 10.1126/scitranslmed.aaa8038

This PDF file includes:

• Fig. S1. Schematic representation of amplified T cell library assay.
• Fig. S2. Sorting strategy of each T cell subpopulation.
• Fig. S3. PCA of functional phenotypes of myelin-reactive CD4⁺CCR6⁻ T cells.
• Fig. S4. Functional phenotypes of myelin-reactive CD4⁺ T cells.
• Fig. S5. Representative tetramer staining and sorting strategy of each library were chosen for single-cell cloning and RNA sequencing.
• Fig. S6. Specificity of myelin-reactive CD4⁺ T cells.
• Fig. S7. Phenotypic analysis of myelin-specific single-cell clones.
• Fig. S8. Cell proliferation of each well from MS patients and healthy controls chosen for RNA sequencing.
• Fig. S9. Correlation of RNA-seq data across biological replicates.
• Fig. S10. Differential expression analysis of myelin-reactive T cells in MS and healthy controls.
• Fig. S11. Correlation scatterplots.
• Fig. S12. Heat maps of selected enriched gene sets identified by GSEA in MS tetramer-positive samples.
• Fig. S13. Histogram showing distribution of the number of times each gene appeared across all gene sets.
• Fig. S14. Heat map of log₂FPKM values for the 224-gene leading-edge set.
• Fig. S15. Enriched canonical pathways and network analysis.
• Fig. S16. Additional network analysis.
• Table S1. Patients with MS and paired healthy subjects information.
• Table S2. Myelin peptides and control peptides used in T cell library assays.
• Table S3. Percent variance explained by each principal component.
• Table S4. GSEA results (FDR < 0.25) for comparison of MS tetramer-positive to MS tetramer-negative.
• Table S5. GSEA results (FDR < 0.25) for comparison of healthy control tetramerpositive to healthy control tetramer-negative.
• Table S6. Curated gene signatures corresponding to Fig. 4C.
• Table S7. Gene sets used for leading-edge analysis to define pathogenic gene signature.
• Table S8. Summary of networks constructed by IPA from pathogenic signature.
• References (51, 52)

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Other Supplementary Material for this manuscript includes the following:

• Table S9 (Microsoft Excel format). Raw data of T cell library assays.
• Table S10 (Microsoft Excel format). Statistical summary of T cell library data.

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