Microarray analysis of RNA processing and modification
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Updated: Jul 20, 2026

Methylated RNA Immunoprecipitation Assay to Study m5C Modification in Arabidopsis
Published on: May 14, 2020
Timothy R Hughes1, Shawna L Hiley, Arneet L Saltzman
1Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.
Abstract:
Most RNAs are processed from precursors by mechanisms that include covalent modifications, as well as the removal of flanking and intervening sequences. Traditional methods to detect RNA processing, such as Northern blotting, reverse-transcribed polymerase chain reaction and primer extension assays, are difficult to apply on a large scale. This chapter outlines several methods for analysis of the processing and modification of RNA using microarrays. These encompass protocols for the application of homemade microarrays and custom-designed commercial inkjet microarrays and are tailored for the large-scale analysis of processing of mRNA, including alternative splicing, as well as for the analysis of processing and modification of noncoding RNA. This chapter also describes practical aspects of microarray design, sample preparation, hybridization, and data analysis.
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