Are there any consequences to using random primers with total RNA in the SenseAMP procedure?
Ribosomal RNA will be amplified when random primers are used. However, provided that the appropriate stringency is maintained, the amplified ribosomal RNA will not bind to a microarray (even if it is labeled). Simply use more senseRNA into the labeling reaction for later hybridization to microarrays. More senseRNA is needed for the labeling reaction to accommodate the portion of senseRNA that is actually the amplified message.
