RNA Fragmentation Reagents (Invitrogen™)

For the fragmentation of aRNA prior to hybridization with oligonucleotide arrays. The protocol is simple, fast and can be completed in less than 20 min. Sufficient Ambion® reagents are included for 200 rxns. Many protocols for using amplified RNA in microarray analysis recommend fragmenting the aRNA prior to hybridization with an oligonucleotide microarray. This fragmentation step improves hybridization kinetics with the arrayed oligonucleotides and can lead to enhanced signal. The protocol is simple. Mix the aRNA with the Ambion® 10X RNA Fragmentation Reagent and heat to 70°C for 15 min. The rxn is then stopped by the addition of the Stop Solution and placed on ice until ready for hybridization with the microarray. The average size of the resulting fragments will be 60-200 nucleotides. Up to 10 μg of RNA can be fragmented in a 10 μL rxn.