Optimized workflow for single-cell transcriptomics on infectious diseases including COVID-19

Abstract

Summary: In December 2019, a new coronavirus, SARS-CoV-2, which causes the respiratory illness that led to the COVID-19 pandemic, was reported. In the face of such a new pathogen, special precautions must be taken to examine potentially infectious materials due to the lack of knowledge on disease transmissibility, infectivity, and molecular pathogenicity. Here, we present a complete and safe workflow for performing scRNA-seq experiments on blood samples of infected patients from cell isolation to data analysis using the micro-well based BD Rhapsody platform.For complete information on the use and execution of this protocol, please refer to Schulte-Schrepping et al. (2020).

Keywords

• Bioinformatics
• Sequence analysis
• Flow cytometry/mass cytometry
• Clinical protocol
• Sequencing
• RNA-seq