Figure S3.

Signatures of COVID-19 severity revealed by bulk RNA-seq, related to Figure 2

Whole blood total RNA-seq for hospitalized COVID-19 patients showing (A) matrix correlation of principal components (PCs) with covariates (B) differentially expressed immunoglobulin lambda chain gene IGLV3-25 and innate viral response gene OAS1 and (C) correlation plot showing the influence of cell proportion on detection of differentially expressed genes. (D) Pathway enrichment for COVID-19 severe and critical versus sepsis using Reactome. Bars indicate 95% confidence intervals. (E-H) Weighted gene correlation network analysis (WGCNA) of whole blood total RNA-seq. (E) Heatmap showing module trait relationships. (F,G) Enrichment of WGCNA modules using gene expression data showing for (F) 64 immune and stroma cell types (xCell), (G) MSigDB canonical pathway genesets, and (H) module eigengene values plotted by patient group. Comparator group abbreviations HV: healthy volunteer; CM: COVID-19 in-patient mild; CS: COVID-19 in-patient severe; CC: COVID-19 in-patient critical; CComm: COVID-19 community case in the recovery phase (never admitted to hospital); Sepsis: in-patient severe and critical sepsis.