FAQ: How long should I incubate the fragmentation reaction?

Fragmentation of RNA is highly sample specific. That is, mammalian RNA will behave differently than plant RNA, which is different than bacterial RNA, etc. Also, there are typically differences in RNA purified by different methods. So it is usually best to perform some pilot experiments to determine the optimal time to fragment your particular RNA samples. Times may vary between 5-30 minutes, and the desired RNA fragment size may also affect the fragmentation time.