Figure 3: Single-cell analysis of lung and peripheral blood samples from patients treated with or without dexamethasone.

a,b, Plot per patient showing the collection of blood (a; N = 7 Dex, 3 NoDex) or TA samples (b; N = 10 Dex, 7 NoDex) overlaid on hospitalization (gray bars) and dexamethasone treatment (pink bars). X-axis shows days of hospitalization (day 0 = admission to UCSF hospital). Dots show the day when sample was collected, colored by Study Day (methods). c,d, UMAP plots of single-cell RNA-seq data from blood (c) or TA (d) samples, clustered and annotated by major immune cell types. e,f, UMAP plots of single-cell RNA-seq data from blood (e) or TA (f) samples, colored by Dex (blue) or NoDex (pink) samples. g,h, log₂ fold difference of gene expression of Dex and NoDex in TA (y-axis) v. blood (x-axis) plotted for Neutrophils (g) and Tregs (h). Significant genes in TA only (blue), blood only (brown), both compartments (red) are shown (adj. p-value < 0.1 & |log₂ fold-difference| > 0.5). Spearman’s correlation R value shown between the two compartments.