The complex mixture of cell types in brain impedes mRNA profiling of specific cellular phenotypes. We have developed approaches to label, harvest and analyze specific cellular phenotypes in the brain. Target cells are either genetically labeled (see Low et al., 2003 SFN Annual Meeting) or are labeled using a neural tracer as in this study. Cortical and dopamine-containing SN neurons were labeled by injection of FG into rat striatum. Five days post-injection rats were perfused and the brains frozen, sectioned and placed on slides. FG-labeled neurons within SN immuno-stained for tyrosine hydroxylase indicating FG had been taken up by the dopamine cells. Labeled SN and cortical cells were harvested from slides by LCM. Neurons from each site were picked, the RNA extracted and made into cDNA containing the T7 RNA polymerase promoter site. Two rounds of amplification were performed and a portion of the final aRNA was reverse transcribed to incorporate Cy-3 or Cy-5 label into cDNA. Differentially labeled cDNA der...