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

• Published in: STAR protocols Vol. 1; no. 3; p. 100233
• Main Authors: De Domenico, Elena, Bonaguro, Lorenzo, Schulte-Schrepping, Jonas, Becker, Matthias, Händler, Kristian, Schultze, Joachim L.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 18-12-2020; Elsevier
• Subjects: Antibody; Bioinformatics; Biomarkers - blood; Clinical protocol; Communicable Diseases - genetics; Communicable Diseases - metabolism; COVID-19 - genetics; COVID-19 - metabolism; Flow cytometry/mass cytometry; Gene expression; Humans; Immunology; Proteomics; Protocol; RNA-seq; RNA-Seq - methods; SARS-CoV-2; Sequence analysis; Sequencing; Single-Cell Analysis - methods; Transcriptome - genetics; Workflow; Clinical protocol; Immunology; RNA-seq; Antibody; Proteomics; Gene expression; Bioinformatics; Sequence analysis; Sequencing; Flow cytometry/mass cytometry
• ISSN: 2666-1667; 2666-1667
• DOI: 10.1016/j.xpro.2020.100233

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).
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•Complete, safe protocol for handling potentially infectious blood samples for scRNA-seq•scRNA-seq application including sample multiplexing and AbSeq protein quantification•Guidelines for flow cytometry analyses of potentially infectious blood samples•Recommendations and code for processing and analysis of multiplexed scRNA-seq data
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.