In the last few decades many efforts have been dedicated to decipher the nature and regenerative potential of neurogenic niches and endogenous stem cells after damage of the central nervous system. In the spinal cord, it has been largely focused on the ependymal region, which hosts neural precursors/stem cells (NSC) in rodents but differs between species and ages. In the current chapter, we detail our protocol to study the gene expression profile of this region using fresh frozen blocks of rat and human post-mortem spinal cords. We describe how to prepare and process those tissues, how to identify and dissect the ependymal region using Laser-Capture Microdissection (LCMD), and how to isolate and amplify RNA with different integrity states to finally obtain enough material for performing gene expression assays using Taqman® Low Density Arrays. LCMD technique maintains tissue integrity allowing for subsequent analysis without manipulation steps that may alter molecular properties of cells and the eventual loss of delicate cell types in comparison with other approaches that require previous disaggregation of the tissue and cell manipulation before isolation.