Figure S1.

Overview of Sample Analysis Pipeline, Major Leukocyte Lineages Definition, and Quantification by CyTOF and MCFC, Related to Figure 1

A, Overview of the analysis pipeline for scRNA-seq and proteomics of COVID-19 samples.

B, High resolution SPADE analysis with 400 target nodes and individual nodes aggregated to the indicated major immune cell lineages according to the expression of lineage specific cell marker such as CD14 for monocytes and CD15 for neutrophils of whole blood samples collected from FLI patients, COVID-19 patients and controls and stained with CyTOF panel 1 and 2, respectively.

C, Boxplots of the composition of total granulocytes and non-classical monocytes within whole blood samples from the second cohort of COVID-19 patients showing either mild (n = 3) or severe disease (n = 7) as well as controls (n = 11) measured by flow cytometry. Statistical analysis was performed using unpaired t test. ^∗∗p < 0.01, ^∗∗∗p < 0.001.