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Exiqon (miRCURY) microRNA microarray - (Jun/22/2006 )

Hi all,

I want to perform microRNA profiling of some cells. Does anyone have any recommendations as to what microarray platform to use? I'm very keen on the Exiqon LNA-modified miRCURY array - does anybody have any positive or negative experience of using this array?

I was also thinking about the Ambion array, but based on previous experience with other Ambion products, I'm being very careful about taking this expensive plunge into the unknown with them.

Thanks for any input!


-miRNA man-

If you need a full scale (sort of HTS approach), every possible miRNA, I'd go with the array technology. There's more literature in general and depending on the product they can be reliable. As you mention Ambion has some issues. I haven't worked with it personally, but I've seen data generated with the assays and it can be highly variable.

If you have an idea of miRNAs of interest, I would suggest ABI miRNA Taqman assays. They are more cumbersome and quite expensive to use in an HTS format for hundreds of miRNA for profiling. But they are fairly sensitive and robust. But again they are more useful as a secondary assay when you find specific miRNAs that are interesting. Let me know what you think.


Yes, I have noticed the Taqman assays (unfortunately they were released just after we invested in the Ambion SYBR system). My personal feeling is to use an array for complete profiling and then use Northern and the Taqman qRT-PCR for validation of the specific miRs of interest. I'm just finding it difficult to decide which array to use (I'll definitely bear your comments on the Ambion system in mind).


-miRNA man-

Good luck and I hope that you find the right system for your application.

From my experience miRNA detection and quantification accuracy will vary depending on company and method (QRT-PCR v. array). I think there is more literature for profiling using arrays. I also think the sheer number of miRNAs you can profile will help to cover those few markers (miRNAs) that are relevant to your tissue type or sample.

A drawback is the scaleability of the arrays. Its easier to put add additional taqman or RT assays as they become available. But running the panel of RT assays can get pretty cumbersome. It seems like everytime you turn around companies are releasing another set of assays as they are dumped into the miranda database.