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The mammalian neocortex gives rise to perception and initiates voluntary motor responses. The cortical laminae are comprised of six distinct cellular layers of local circuit neurons and projection neurons. To explore molecular identities of the distinct cortical projection neurons, discovery-orientated genomic approaches have been adopted. Microarray analysis of dissected cortical tissues has been applied to identify cortical layer markers. Early neuronal cells were sorted by FACS from GFP-labeled embryonic brains for gene expression profiling. Laser capture microdissection of retrograde-labeled projection neurons, when coupled with optimal RNA amplification technology, has become a valuable strategy for neuronal isolation and gene expression analysis in differentiated neurons. RNA sequencing technology is promising not only for the determination of gene expression, but also for discovery of posttranscriptional modifications of the complex neural system. There is no doubt that advances in genomic studies are opening up novel research avenues for our understanding of the cortical neuronal functions.