Fig 1: Cells isolated from brochoalveolar lavage of severe COVID-19 patients are enriched in TGFB1-expressing T and CD14-positive cells.Bronchoalveolar lavage (BAL) cells for single cell sequencing were enriched for CD45+ cells via MACS and live cells were further sorted using FACS (gating strategy in Supplementary Fig. 7a). a UMAP of 5459 cells representing clusters containing T cells, B cells, and CD14-expressing cells from patient #1 on day 59 following ICU admission. B and T cell cluster identification based on BCR/TCR, CD19, CD3E, CD4, and CD8A expression (see Supplementary Fig. 7b). UMAP representation of expression of TGFB1, IL21, CD40LG, and IFNG. b UMAP coordinates and clustering was computed for 433 and 2723 cells from patient #9 on days 31 and 46 following ICU admission, respectively. UMAP representation of expression of TGFB1, IL21, CD40LG, and IFNG at the two different time points is shown side by side.