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

STAR Protoc. 2020 Dec 16;1(3):100233. doi: 10.1016/j.xpro.2020.100233. eCollection 2020 Dec 18.


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: Antibody; Bioinformatics; Clinical protocol; Flow cytometry/mass cytometry; Gene expression; Immunology; Proteomics; RNA-seq; Sequence analysis; Sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biomarkers / blood
  • COVID-19* / genetics
  • COVID-19* / metabolism
  • Communicable Diseases* / genetics
  • Communicable Diseases* / metabolism
  • Humans
  • RNA-Seq / methods*
  • SARS-CoV-2
  • Single-Cell Analysis / methods*
  • Transcriptome / genetics*
  • Workflow


  • Biomarkers