Protocol for high-quality single-cell RNA-seq from tissue sections with DRaqL.

Single-cell RNA sequencing (scRNA-seq) combined with laser capture microdissection (LCM) offers a versatile framework for comprehensive transcriptomics from tissue sections. Here, we present a detailed protocol for DRaqL (direct RNA recovery and quenching for LCM) in combination with Smart-seq2 (DRaqL-Smart-seq2), which enables high-quality RNA sequencing for single cells obtained from alcohol-fixed murine ovarian sections. Additionally, we provide an optional procedure for scRNA-seq from formalin-fixed sections (DRaqL-Protease-Smart-seq2). We outline key steps for cell lysis, cDNA amplification, and sequencing library preparation. For complete details on the use and execution of this protocol, please refer to Ikeda et al..