will fragmentation buffer of mRNA-seq cut 200nt of my sample into small pieces?

[ziseputi]

Hi, Everyone,

More than 60% of my RNA sample is about 30-200nt, and other are from 200nt-2000nt, I am wondering whether the fragmentation buffer of mRNA-seq will cut 200nt of my sample into small pieces? so I can not sequence this part of RNA, or the fragmentation is random, so I can still get the sequence information of them? what is the best strategy if I want to get all the information of the RNA, is it necessary if I sequence the first library without fragmentation and the second with fragmentation? or it is not necessary to do so as the 200nt RNA will still exist? I am going to use illumina reagents. Thanks.

[luc]

Hi, the fragmentation is through a chemical reaction (interaction of the RNA with metals [e.g. Mg2+]), thus it should be random.
Nevertheless the most efficient approach seems to sequence at least two length based fractions of the RNA separately.