miRNA profiling - (Sep/18/2008 )
Hello!
I was wondering what the cheapest and/or most efficient way of miRNA profiling is? I know there are miRNA extraction kits like mirVana to obtain the miRNA in a particular sample, say wt and KO and then id like to compare the two.
Does anyone work in this field? What are ones options? I think arrays would be the most time consuming and expensive right? But maybe the coolest? hehehe
Ideas? Literature? I could use anything im suddenly in charge of this project and I dont want to order any kits before I have traced out some kind of strategy.
Im really curious as to what some of you have to say,
thank you if you reply! 
Taqman microRNA array is optional. It can be done in 1.5 h
I was wondering what the cheapest and/or most efficient way of miRNA profiling is? I know there are miRNA extraction kits like mirVana to obtain the miRNA in a particular sample, say wt and KO and then id like to compare the two.
Does anyone work in this field? What are ones options? I think arrays would be the most time consuming and expensive right? But maybe the coolest? hehehe
Ideas? Literature? I could use anything im suddenly in charge of this project and I dont want to order any kits before I have traced out some kind of strategy.
Im really curious as to what some of you have to say,
thank you if you reply!
If you want the coolest option, I'd definitely say that Solexa or 454 high throughput sequencing is the coolest, also most expensive, but probably gives you the most data. Microarray is also good for high throughput, main disadvantage to 454 is that you can't find/profile novel miRNAs this way. Saying that, we've used the CombiMatrix arrays with good results on single colour dye experiments. Exiqon arrays are also supposed to be good.
Like microlight said, TaqMan is fast, but only if you have a couple of miRNAs in mind that you want to profile. Otherwise I don't think that it is so high throughput and better suited to validation or study of a miRNA that you identify through the 454/array.
Hey thanks!
I read about it on the web.........so the coolest way is to do high-throughput sequencing......uhm..........we have a core facility in the institute that provides a miRNA profiling service, I asked and they have approx 400 on the array and its around 200 per sample.
Thing is.......I have mouse cell lines, im wondering how much sense it makes to profile or sequence two mouse cell line samples, say wildtype and tumor and then obtain miRNAs that are associated with my protein of interest.
What do you think??
I think both options would probably be ok. The thing with the sequencing is that is maximizes your chances of finding a miRNA that fits into your pathway because you could find novel miRNAs. I suppose it is a trade-off between this and the costs involved.
uhm......yes....I will inquire about prices, it would be much more exciting to identify a new one than just a difference in the expression profile. I think I will look into literature and then decide, maybe a similar approach has already been done.
Thank you!
I wonder if anyone has tried this kit:
mirVana™ PARIS™
Isolate Total RNA, Small RNA, and Protein from the Same Sample,
sounds pretty cool and its not that much more expensive that the regular mirVana kit