snPATHO-seq: unlocking the FFPE archives for single nucleus RNA profiling [snRNA-seq]

FFPE tissue samples have long been considered challenging for sc-/sn-RNA sequencing assays. In this study, we developed a novel snRNA-seq workflow, snPATHO-seq, for FFPE tissue samples utilising isolated high-quality nuclei from FFPE samples and 10X Genomics FLEX chemistry. The snPATHO-seq demonstrated consistent performance with the established 10X Genomics 3' assay. In addition, it allows more accurate single-nucleus and spatial transcriptomics integration with the FFPE Visium dataset generated from the same FFPE block. We envision this new protocol can facilitate the transcriptomic interpretation of millions of FFPE archives generated and simplify the sample collection process and data generation. Overall design: Snap frozen and FFPE samples from a wide range of tissue types were dissociated for nuclei isolation and characterised using 10X Genomics 3' v3.1 or FLEX chemistry for direct workflow comparison.