KB000721: Can Total RNA be used in a Labeling / Amplification Procedure? - Microarray Labeling 

Probably. We recommend the use of poly-A+ RNA since we can readily quantitate the amount of RNA substrates added to the reaction and the amount of cRNA produced in the reaction so we know how well the amplification is working. For total RNA, we suggest you adjust the amount of total RNA that its contains to 200ng polyA+ RNA, for example, if you expect the percentages of polyA+ RNA in your sample is 3%, 6.6ug of total RNA will be added to the labeling reaction.