Previous studies have shown that long-term retention of fear extinction requires the medial prefrontal cortex (mPFC). Inhibition of NMDA receptors (Burgos-Robles et al., SFN, 2004) or protein synthesis (Santini et al., 2004) in the mPFC impairs consolidation of fear extinction. Here we used Agilent 22K rat oligonucleotide microarrays to identify genes that are regulated within the mPFC during extinction. Four experimental groups were studied: 1) Rats receiving tone fear conditioning on Day 1 and extinction training on Day 2 (EXT); 2) Same as above but with a systemic injection of the NMDA antagonist CPP (10 mg/kg) prior to extinction (EXT-CPP); 3) Rats that received acquisition but no-extinction (No-EXT); 4) Rats given a full set of tones but never shocked. Extinction was given in a different context than conditioning, and rats were sacrificed 30 min after extinction training. Total RNA was obtained from the mPFC, linearly amplified, and labeled using fluorescent dyes Cy3 or Cy5. Data from two biological r...