We have recently started using the Affymetrix Human Gene ST 1.1 and Mouse Gene 1.1 ST arrays. These arrays are designed primarily to measure expression of well-annotated genes, not microRNAs. However, as of annotation revision 31, the Mouse Gene ST chip lists 341 microRNA probesets. For example, probeset 10409709 is annotated as Mir7-1, with 28 probes covering the transcript. Presumably these probes measure the full-length transcripts before processing.
Has anyone actually used these probesets to look at microRNA expression? Specific questions:
- Normalization: Did you just use gcRMA? We've some experience using ABI assays to measure microRNA expression, and the normalization methods are quite different there.
- Results: How do the results compare results to custom-designed assays? Do the probes work?
Anyone who has seen a reference to using these arrays for miRNA analysis in the literature, I'd be very grateful. We are considering changing our favorite RNA extraction protocol to take advantage of these probes, as normally we would discard microRNA-sized RNA. Is it worth the change?
NOTE: This question is distinct from the one recently asked. I know we can buy dedicated microarrays to measure microRNA levels; that's not what this question is about.