A method of stripping custom microarrays

Our genome wide analyses of microRNA expression profiles involve the hybridization of fluorescently labeled RNA samples to custom made, DNA microarrays based on the GAPSII coated slides. We describe a simple and effective method to regenerate such custom microarrays. Our protocol entails the use of a very low concentration of sodium hydroxide in a low salt buffer to strip RNA molecules from the arrays. The solution is also capable of removing DNA molecules hybridized to the slides, while preserving the slide coating and printed DNA probes. Slides can be stripped and reused at least twice without significantly sacrificing data quality. Keywords: expression study, new vs. stripped array comparison There are two stripping conditions in this study (1mM NaOH and 2mM NaOH in SSC buffer). For 1mM NaOH treatment, new, once-, twice-, and triple-stripped arrays are studies. For 2mM NaOH treatment, new and once-stripped arrays are measured.