Expression profiling with oligonucleotide arrays: technologies and applications for neurobiology

• Published in: Neurochemical research Vol. 27; no. 10; pp. 1005 - 1026
• Main Authors: Sendera, Timothy J, Dorris, David, Ramakrishnan, Ramesh, Nguyen, Allen, Trakas, Dionisios, Mazumder, Abhijit
• Format: Journal Article
• Language: English
• Published: United States Springer Nature B.V 01-10-2002
• Subjects: Brain - physiology; Gene Expression Profiling - methods; Humans; Neurobiology - methods; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis; Reproducibility of Results; RNA
• ISSN: 0364-3190; 1573-6903
• DOI: 10.1023/A:1020948603490

DNA microarrays have been used in applications ranging from the assignment of gene function to analytical uses in prognostics. However, the detection sensitivity, cross hybridization, and reproducibility of these arrays can affect experimental design and data interpretation. Moreover, several technologies are available for fabrication of oligonucleotide microarrays. We review these technologies and performance attributes and, with data sets generated from human brain RNA, present statistical tools and methods to analyze data quality and to mine and visualize the data. Our data show high reproducibility and should allow an investigator to discern biological and regional variability from differential expression. Although we have used brain RNA as a model system to illustrate some of these points, the oligonucleotide arrays and methods employed in this study can be used with cell lines, tissue sections, blood, and other fluids. To further demonstrate this point, we provide data generated from total RNA sample sizes of 200 ng.