Science Immunology

The PDF file includes:

• Fig. S1. Sorting strategy and clustering information of BAL fluid immune cells from all patients.
• Fig. S2. Clustering information of blood T cells from all patients.
• Fig. S3. Flow cytometry of cells from peripheral blood and BAL fluid.
• Fig. S4. Location of T cells in the lung of COVID-19.
• Fig. S5. Clustering information of BAL fluid T cells from all patients.
• Fig. S6. Clonal expansion analysis of BAL fluid T cells from all patients.
• Fig. S7. Subclustering of clonally expanded BAL fluid CD4 T cells from all patients.
• Fig. S8. Clustering information of BAL fluid myeloid cells from all patients.
• Fig. S9. Cell-cell interaction of T cells with myeloid cells and epithelial cells.
• Fig. S10. Cytokine levels in BAL fluid.
• Table S1. Baseline characteristics and disease-related parameters of COVID-19 patients and controls.
• Table S2. Relevant medication of COVID-19 patients and controls.
• Table S3. Baseline characteristics of the Halle cohort.

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Other Supplementary Material for this manuscript includes the following:

• Table S4. CITE-seq antibodies and barcodes (Excel file).
• Table S5. Gene sets (Excel file).
• Table S6. Raw data file (Excel file).