Kay Pogue-Geile, National Surgical Adjuvant Breast and Bowel Project, Pittsburgh, Pa.
Developing prognostic profiles for breast cancer using tumor samples obtained from clinical trials.
Nucleic acids are degraded and modified by the formalin fixation process used in paraffin-embedded tissue.
Treating embedded sections with xylene gets rid of the paraffin, and heating can remove most cross-linked proteins. You can use commercial kits, such as those available from Roche or Ambion, to clean away the formalin and extract the RNA.
After these treatments only 100- to 200-base fragments remain, some with short poly-A tails, and some without. Traditional reverse-transcription using an oligo-dT primer won't work very well on such degraded RNA. So, Pogue-Geile uses a kit from Rubicon Genomics to add adapters to both ends of...