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

Key Points

• The aim is to optimize sample preparation and library synthesis for single-nuclei multiomic profiling from limited primary tissues.
• Protocols for dissociating head and neck squamous cell carcinoma and matched-normal tissues using a mechanical-enzymatic workflow.
• Minimizing ambient nucleic acid background via red blood cell lysis and DNase-I treatment.
• Isolating intact nuclei through density gradient centrifugation and employing modified sn-ATAC and 3′-GEX indexing PCR for size selection.
• Successfully increased library complexity for multiomic profiling from limited tumor samples.
• Achieved significant reduction in debris content enhancing nucleic acid quality.
• Demonstrated robust protocols for single-nuclei isolation, improving transcriptomic and epigenomic analysis outcomes.