Protocol to maximize single-nuclei multiome library complexity for limited primary tissues via optimized sample preparation and library synthesis

Single-nuclei multiomic profiling of clinical biopsies is often hindered by limited tumor mass and high debris content. Here, we present a protocol for the dissociation of head and neck squamous cell carcinoma (HNSCC) and matched-normal tissues using a mechanical-enzymatic workflow. We describe steps for minimizing ambient nucleic acid background by red blood cell (RBC) lysis and DNase-I treatment and for removing cellular debris using density gradient centrifugation. We then detail procedures for isolating intact nuclei and modified single-nuclei assay for transposase-accessible chromatin sequencing (sn-ATAC) and 3′-GEX (gene expression) indexing PCR and size selection to maximize library complexity.