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Related Experiment Video

Updated: Nov 23, 2025

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
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Optimized workflow for single-cell transcriptomics on infectious diseases including COVID-19.

Elena De Domenico1,2, Lorenzo Bonaguro2,3, Jonas Schulte-Schrepping2,3

  • 1German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany.

STAR Protocols
|December 30, 2020
PubMed
Summary
This summary is machine-generated.

This study outlines a safe workflow for single-cell RNA sequencing (scRNA-seq) on blood samples from COVID-19 patients. It details a complete protocol from cell isolation to data analysis for studying SARS-CoV-2.

Keywords:
AntibodyBioinformaticsClinical protocolFlow cytometry/mass cytometryGene expressionImmunologyProteomicsRNA-seqSequence analysisSequencing

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Area of Science:

  • Virology
  • Immunology
  • Genomics

Background:

  • The emergence of SARS-CoV-2 in December 2019 necessitated stringent safety protocols for handling infectious materials.
  • Limited understanding of SARS-CoV-2 transmissibility, infectivity, and pathogenicity required specialized experimental approaches.

Purpose of the Study:

  • To present a comprehensive and safe workflow for single-cell RNA sequencing (scRNA-seq) on blood samples from patients infected with SARS-CoV-2.
  • To provide a standardized protocol for researchers studying the molecular and cellular responses to COVID-19.

Main Methods:

  • Utilized the micro-well based BD Rhapsody platform for scRNA-seq experiments.
  • Developed a complete workflow encompassing cell isolation, library preparation, and data analysis.
  • Emphasized safety precautions for handling samples from patients with a novel pathogen.

Main Results:

  • Successfully established a safe and complete scRNA-seq protocol for processing blood samples from COVID-19 patients.
  • The workflow enables detailed molecular and cellular analysis of the host response to SARS-CoV-2 infection.

Conclusions:

  • The presented workflow ensures safe and efficient scRNA-seq analysis of SARS-CoV-2 infected patient samples.
  • This protocol facilitates in-depth investigation into the pathogenesis and host-cell interactions of COVID-19.