How can nuclei quality be evaluated, especially for frozen tissue samples?
2026-06-23
Answer:
For frozen tissues, nuclei quality cannot be defined as strictly “pass” or “fail,” because sample integrity before nuclei isolation cannot be directly assessed. However, several parameters can be used to evaluate physical nuclei integrity and suspension cleanliness before proceeding.
Recommended evaluation criteria (using a fluorescence cell counter such as SeekMate Tinitan FL with AO/PI staining):
Metric | Recommended Range | Interpretation |
Viability (PI-positive nuclei) | <5% | PI-positive nuclei >10% suggests severe nuclear membrane damage |
Aggregation rate | <15% | High aggregation increases doublet risk |
Nucleated cell rate | >50% | Low values indicate excessive debris or RBC contamination |
Nuclear membrane integrity | >80% intact morphology | Nuclei should display smooth boundaries without leakage |
Debris/background level | Low | Excess debris can absorb transposase and reduce reaction efficiency |
Additional notes:
- Aggregates can often be reduced by gentle pipetting or filtration through a 35–40 μm strainer
- Excessive debris is associated with lower ATAC signal quality and reduced transposition efficiency
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