SnFFPE-Seq: towards scalable single nucleus RNA-seq of formalin-fixed paraffin-embedded (FFPE) tissues

Profiling cellular heterogeneity in formalin-fixed paraffin-embedded (FFPE) tissues is key to characterizing clinical specimens for biomarkers, therapeutic targets, and drug responses. Here, we optimize methods for isolating intact nuclei and single nucleus RNA-seq from FFPE tissues in the mouse brain, and demonstrate a pilot application to a human clinical specimen of lung adenocarcinoma. Our method opens the way to broad applications of snRNA-Seq to archival tissues, including clinical samples. Intact nuclei were isolated from scrolls of FFPE specimens of the mouse cortex, after deparaffinization, rehydration, and tissue lysis