Should I choose single cell or single nucleus RNA sequencing?

Single cell RNA-seq is recommended for fresh cell suspensions, fresh tissue that can be dissociated into intact, viable cells, and cryopreserved cells such as PBMCs. Single nucleus RNA-seq is recommended for frozen tissue and for tissues that are difficult to dissociate, such as brain, muscle, pancreas, liver and tumor biopsies.  

The right choice depends on the research goals, target cell types and tissue characteristics. In a Singleron comparison on mouse brain tissue, single cell RNA-seq captured a larger proportion of immune cells, especially microglia, while single nucleus RNA-seq captured more adherent cells such as excitatory neurons.

Single nucleus RNA-seq also allows tissue to be snap-frozen immediately, which is valuable for clinical samples and time-sensitive experiments: frozen tissue can be stored for up to 6 months. For single cell RNA-seq, fresh tissue can be stored for up to 3 days in sCelLiVE^® Tissue Preservation Solution at 4 °C. For FFPE archived tissue or freshly fixed tissue, Singleron’s RetroSCOPE^® kit generates single nucleus data in a probe-independent way, capturing both coding and non-coding RNAs.

For an in-depth comparison between single cell and single nucleus RNA sequencing, check out the comparison data in the scRNA-seq vs snRNA-seq technical note.