- Avoid methods based on organic solvents (Trizol)
- Avoid harsh chaotropic salts (i.e. guanidinium)
- Avoid detergents that impact downstream quantitation by UV and/or Qubit (e.g. Triton X-100)
- Do not rely on RIN to quantitate the integrity of an FFPE-derived sample, use DV200 instead.
- Use a kit or method that removes chemical modifications from formalin. Do not raise the temperature to 80˚C or above. Even short times at this temperature will significantly lower integrity.
- Be wary of Qubit and Nanodrop concentrations because of the possibility of contamination by organic molecules or DNA.
- Use qPCR to quantitate your RNA, and always look carefully at melt curves to determine whether nonspecific amplification may have occurred.
What do I need to know when extracting RNA from FFPE samples?
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