Work

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

Year: 2025

Type: article

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 • Steps for tissue dissociation and cell suspension preparation from resected liver/HCC • Procedures for 10× Genomics single-cell library construction and sequencing workflow • Instructions for FASTQ QC, Cell Ranger alignment (human + HBV), and count matrix • Guidance on HBV read parsing and genome coverage visualization Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. 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.

Source: STAR Protocols

DOI: 10.1016/j.xpro.2025.104230

Authors: Lina Liu, Liyu Chen, Lingyun Zhou

Institutions: Sichuan University, West China Medical Center of Sichuan University, West China Hospital of Sichuan University

Language: English

Topic: Hepatitis B Virus Studies

Subfield: Epidemiology

Field: Medicine

Domain: Health Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $1,550