Nuclei isolation

The Spatial Technologies Unit performs nuclei isolation in house - a capability few facilities offer - across fresh, frozen, and FFPE material. Isolating nuclei internally, rather than requiring investigators to deliver ready-made suspensions, gives the unit control over quality, provenance, and turnaround, and lets it take on tissue types that are difficult for single-cell work.

Sample types

The unit supports several nuclei-preparation strategies to match the sample:

• Fresh or fixed cell suspensions.
• Fresh, or pre- and post-fixed, nuclei from frozen tissue.
• Nuclei from FFPE tissue.

Low-viability live-cell suspensions can be enriched for viable cells to improve result quality. Nuclei isolation has been established across a wide range of tissues, including types considered challenging for single-cell work such as liver, skin, adipose, and decalcified samples.

snPATHOseq: single-nucleus RNA-seq from FFPE

For FFPE material, the unit runs snPATHOseq, a protocol it co-developed and validated across more than ten tissue types (Wang et al., Communications Biology, 2024). The STU was the first facility in the US to offer single-nucleus RNA-seq from FFPE (2022) and has provided it at production scale since. On the Flex platform, snPATHOseq gives data quality comparable to frozen tissue.

For frozen samples with RIN below 4 but DV200 above 30%, an adapted snPATHOseq protocol is available with no loss of quality.

Requirements

• Tissue for single-nucleus RNA-seq: more than 50 mg, or 30 µm of FFPE.
• RNA quality: RIN greater than 4 (fresh and frozen); DV200 greater than 30% (FFPE).

Isolated nuclei feed the unit's single-cell and single-nucleus assays. Contact the unit to scope a project.