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  3. Protocol for quantifying hepatitis B virus transcript abundance and genomic segment distribution from single-cell RNA-seq

Protocol for quantifying hepatitis B virus transcript abundance and genomic segment distribution from single-cell RNA-seq

  • STAR Protoc. 2025 Nov 27;6(4):104230. doi: 10.1016/j.xpro.2025.104230.
Lina Liu 1,  Liyu Chen 2,  Lingyun Zhou 3
Affiliations

Affiliations

  • 1 Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, China; Laboratory for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China.
  • 2 Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, China. Electronic address: [email protected].
  • 3 Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, China. Electronic address: [email protected].
PMID: 41313688 DOI: 10.1016/j.xpro.2025.104230
Abstract

Hepatitis B virus (HBV) drives liver disease progression. Here, we present a protocol for Sequencing single cells from HBV-infected liver tissue, producing two complementary outputs: quantitative per-cell HBV transcript abundance and a genome-wide map of read distribution. We describe steps for tissue dissociation and purification, single-cell RNA Sequencing (RNA-seq), library construction, Sequencing, and data processing. We then detail procedures for HBV expression and genome distribution analysis. This protocol enables detailed analysis of viral expression patterns and HBV-host interactions at single-cell resolution. For complete details on the use and execution of this protocol, please refer to Zhou et al.1.

Keywords

Bioinformatics; Cell biology; Gene expression; Health sciences; Molecular biology; Sequence analysis; Single cell.

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