Do you have any data showing that high-quality results can be obtained using 1 μg of total RNA as starting material following the One-Cycle labeling protocol?
Extensive analysis was carried out at Affymetrix to examine the sensitivity and reproducibility of the protocol for 1 μg of starting material. The results demonstrate comparable cRNA length (by Bioanalyzer electrophoresis), sensitivity (P% call and spike-ins), and reproducibility (by Signal correlation, call concordance, false change) compared with using 5 μg of total RNA as starting material. In addition, the Change calls analyzing two different samples were also highly consistent within the assay.
For large-scale studies involving many different samples, it is still advisable to normalize the starting materials, and always use the same starting quantity to obtain the most direct and reliable comparison analysis results.