Can frozen tissue be used for SeekOne DD Multiome ATAC + RNA?

Answer:
Yes, but only under specific circumstances and with elevated experimental risk. Fresh samples are strongly preferred whenever possible.

Frozen tissue should only be considered when at least one of the following conditions applies:

• Fresh tissue cannot be processed immediately
• The target cell type is difficult to dissociate into intact single cells
• Tissue has already been cryopreserved using a validated workflow (rapid freezing within 2 hours after collection, followed by storage at −80°C)

Potential risks include:

• Freeze–thaw damage to nuclear membrane integrity
• Chromatin disruption or mechanical damage
• Reduced transposase accessibility, potentially resulting in lower TSS enrichment scores
• RNA degradation risk, requiring RNA integrity assessment before the experiment (recommended RIN > 7)

Fresh tissue is preferred because chromatin accessibility is highly dynamic. Significant chromatin remodeling can occur within minutes after tissue dissociation due to stress responses, transcription factor activation, metabolic changes, and cell death processes. Even storage on ice cannot completely prevent these effects.

For optimal biological fidelity, tissues should ideally be processed on the day of collection as quickly as possible (dissociation → nuclei extraction).