3.0 years ago by
Unfortunately, Agilent doesn't place their microarray designs in convenient locations such as GEO Browser. You will need to register for Agilent's eArray website. Once registered and logged in, you can obtain the probe design files for their commercial arrays.
Also, beware that microRNA probes bind more miRNAs than what you are interested in. For this reason, Agilent designs multiple probes for each miRNA. For example, hsa-mir-300 has four probes on a particular microarray that I've worked with:
It's the same probe sequence, but each probe differs in length by 1 nucleotide to another probe. The shorter the probe is, the more specific it is to the miRNA it is designed for and the less unwanted miRNAs it binds. But, there's no information about what other miRNAs each probe binds to and in what proportion. The proportion of incorrect binding also varies from one experiment to the other, because in some experiments, the cells don't express the cross-hybridising miRNAs but in other experiments, they do. Microarrays aren't a good technology for measuring miRNAs because of cross-hybridisiation problems. miRNA-seq would give clear results since there is no problematic hybridisation involved.
You should read the manufacturer's technical overview to understand the limitations of miRNA microarrays before commencing your analysis of them.