CAN I USE RIBOSOMAL RNA SEQUENCES AS POSITIVE CONTROLS?
We do not recommend it for gene expression studies in eukaryotic organisms, because the standard mRNA amplification methods (based on oligo(dT) primers) should dramatically reduce the proportion of rRNA in the sample. This reduction may be non-uniform for different samples, different amplification reactions, and different inputs of total RNA. Variable results of this selection against rRNA make it a poor control for array data normalization.
