Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful technique for exploring cellular heterogeneity and host-pathogen interactions. This protocol details the Zika virus (ZIKV)-targeted scRNA-seq workflow for preparing high-quality single-cell suspensions from the whole brain tissues of neonatal mice, high-quality single-cell sorting, cDNA reverse transcription, amplification, ZIKV enrichment and host transcriptome library preparation, and sequencing dataset integration in downstream analysis to complete the quantification of ZIKV RNA in individual cells. Key features • Preparation of high-quality single-cell suspensions from the whole brain tissues of neonatal mice. • ZIKV-specific magnetic beads for using the ZIKV and host cell RNA capture. • ZIKV enrichment and host transcriptome library construction, providing a framework for quantifying viral load within individual cells. • Integration of viral enrichment and host transcriptomic datasets enables the visualization and quantification of ZIKV at single-cell resolution.