ABSTRACT
This chapter presents the use of high-density arrays of relatively short, specifically chosen, in situ synthesized deoxyribonucleic acid (DNA) oligonucleotides on glass and their use for parallel gene expression measurements. Systematic and large-scale measurements of gene expression in multiple brain regions are helping to lay the foundation for asking system-wide questions concerning brain structure and function at the molecular and genetic level. Nucleic acid arrays have been constructed for a wide variety of different organisms and have been used successfully to measure transcript abundance in many different experiments. The advantage of having multiple, different oligonucleotide probes is that they serve as independent detectors for the same gene. One advantage of using shorter, specifically chosen oligonucleotide probes rather than longer complementary DNA is a greater ability to discriminate between genes with similar sequences. The extent of change in expression level for any gene is commonly given as the “fold change.”
