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What do I need to know when extracting RNA from FFPE samples?

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  • 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.

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