Does SeekOne DD Multiome ATAC + RNA support fixed samples?

Answer:
The kit does not support fixed tissue samples, including formalin-fixed tissues or paraformaldehyde-fixed (PFA-fixed) tissues. However, the workflow is compatible with PFA-fixed nuclei (freshly isolated nuclei followed by immediate PFA fixation).

This strategy is particularly useful for tissue types with rapid RNA degradation, where standard fresh-nuclei workflows may result in relatively low median gene counts. Immediate fixation after nuclei isolation can substantially reduce RNA loss and improve transcript preservation.

Potential tradeoffs include:

• Slight reduction in chromatin accessibility signal intensity
• Mild decreases in metrics such as TSS enrichment scores

Based on internal validation experience, the following tissue types have shown improved RNA preservation with this workflow:

• Gastric tumors and adjacent normal tissues
• Colorectal tumors and adjacent normal tissues
• Esophageal cancer tissues
• Liver tissues, especially fibrotic or diseased samples
• Cervical cancer tissues
• Aged mouse tissues (e.g., uterus and lung)
• Spleen
• Subcutaneous tumors

Important notes:

• The workflow for PFA-fixed nuclei differs from the standard multiome protocol and requires additional de-crosslinking and secondary reverse transcription steps.
• A dedicated protocol is available upon request from technical support.
• Additional reagents beyond the standard SeekOne™ DD Single Cell Multiome ATAC + RNA Kit are required.