Single-cell multiomics revealed the dynamics of antigen presentation, immune response and T cell activation in the COVID-19 positive and recovered individuals

We performed scRNA sequencing to understand the cellular heterogeneity and immune response landscape behind COVID-19 pathophysiology. We combine this with Ab-Seq, oligo-attached antibody based quantification of cell surface proteins to better understand the cell type and state of the cells. Samples were multiplexed using BD single-cell multiplexing kit (Human) in order to measure these data simultaneously Overall design: PBMCs were isolated from Healthy (n = 4), COVID-19 (n = 16) and recovered (n = 13) individuals, using BD vaccutainers cell prepataion tubes. PBMCs were isolated as per manufacturer's recommendation, and stored for future use. Samples were multiplexed using BD single cell multiplexing kit (Human), followed by tagging with a pool of 40 oligo-attached antibody for surface markers (Ab-Seq). Around 30000 cells were loaded per cartridge, followed by cell lysis, cDNA synthesis and final library preparation using BD WTA amplification kit as per manufacturer's recommendation. A poly-A transcripts library (WTA), Ab-Seq library and library from oligos of Sampe multiplexing kit (SMK) were constructed from each batch, and were sequenced on NovaSeq 6000 platform.

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