Protocol for minimized-bias profiling of liver and visceral adipose tissue in mice using integrated single-nucleus RNA sequencing

Single-nucleus RNA sequencing (snRNA-seq) enables transcriptomic profiling of tissues that are difficult to dissociate. Here, we present an integrated protocol combining tissue-specific nuclei extraction and selective enrichment to isolate high-quality nuclei from fresh mouse liver and visceral adipose tissue (VAT). We describe steps for single-nucleus extraction, magnetic enrichment, BD Rhapsody capture, cDNA synthesis, whole-transcriptome amplification, index PCR, library quality control, and shallow sequencing-based assessment of cell-type recovery, while separating whole-liver and non-parenchymal cell workflows to reduce dissociation bias.