Single cell multi-omic analysis of human innate immune cells stimulated with SARS-CoV-2 BA.1.

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a) A schematic representation of single cell multi-omic workflow is represented. Peripheral blood mononuclear cells (PBMC) were collected from healthy donors and enriched in HLA-DR+/NK cells through negative selection using CD3/CD19 magnetic beads. Cells were cultured for 16 hours (h) or stimulated with SARS-CoV-2 Omicron BA.1 (MOI= 0.04), the TLR7/8 agonist R848 (5 μM), the TLR9 agonist type C CpG (3 μg/ml) or left untreated as negative control (ctr). BD Rhapsody system was used to prepare single-cell libraries, then sequenced on an Illumina NovaSeq platform. Data were filtered and identified differentially expressed genes (DEG) were used to infer pathway analysis. The scheme was created with the licenced version of BioRender.

b, c) The uniform manifold approximation and projection (UMAP) presentation of the merged samples (b) and cell types (c) were clustered by gene signature after preprocessing. Each dot corresponds to a single cell and is colored according to experimental condition (a) or cell type (b). 
 

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