GSE161918
Time-resolved Systems Immunology Reveals a Late Juncture Linked to Fatal COVID-19
COVID-19 exhibits extensive clinical heterogeneity ranging from asymptomatic infection to death. Unraveling the basis of immune response differences across individuals is critical for developing effective therapeutics and prophylactics. We longitudinally assessed 192 surface protein markers, the transcriptome, and T-cell receptor sequence profiles simultaneously in single peripheral immune cells from COVID-19 patients, and compared to age-matched healthy control samples. Overall design: Peripheral blood mononuclear cells from 33 COVID19 patients and 14 age-matched healthy controls were profiled using multi-modal single cell RNAseq (surface protein staining (Biolegend TotalSeq-C lyophilized panel), mRNA, and T cell recpetor VDJ regions) using the 10x Genomics Chromium system. Individual patients samples, in some cases with multiple samples per donor from different timepoints during disease, were combined and ran together in several lanes of the 10x system, and assignment of the individual cells to a donor and timepoint was done using a combination of SNP and antibody hashtags. SNP calls per donor were determined from bulk level RNAseq data of the individual samples. A single sample, CHI014, was included across the three batches as a technical control, but not used in further analysis. Additionally, a healthy control donor, SHD8, was excluded from further analysis upon finding lymphoma-like B cells in this sample; the HDML_bc and HDVO_bc samples were included to test an alternate cell freezing protocol, and also not used in further analysis.