Why does SeekSpace use nuclei instead of whole cells?

Answer:
SeekSpace is primarily based on single-nucleus spatial transcriptomics.

Spatial workflows are commonly performed on frozen tissue sections, where intact cells are more prone to rupture during tissue processing. In contrast, nuclei are structurally more stable and can often be isolated more reliably.

In addition, many tissue types — including brain tissue, fibrotic tissue, adipose-rich tissue, and certain solid tumors — are difficult to dissociate into high-quality intact single cells, whereas high-quality nuclei can generally be recovered more consistently.

A nucleus-based workflow also helps reduce dissociation-induced stress transcriptional artifacts and cell-type bias introduced during tissue dissociation.

Single-nucleus RNA sequencing data commonly exhibit:

• Higher proportions of intronic reads
• Lower detection of some cytoplasmic RNAs

These are expected characteristics of single-nucleus sequencing and do not indicate experimental failure.