Choosing the right refrence sample for microRNA array - (Dec/13/2009 )

I am planning to do a microRNA profiling for two samples with two genotypes (G1 and G2), using Exiqon microRNA microarray v.11.
For a dual-color common reference design, what is the best reference sample? I was told that a pool of both G1 and G2 can serve as common reference, but since I am looking at differential expression in only two samples, I am afraid I will loose some of the actual differences. (for example, mir-2 has a two-fold change in G2 compared to G1, but in common reference design it will show a 1.5 fold change). Am I right?

Should I make the common reference with more than two types of genotoypes? Or they have to be a pool of samples of interest?

thanks for your help,

Kaveh

I think the better way to go with this problem is to do 3 arrays in single color so that you have independent datasets which can be inter-compared with any other sample , so that you get an unbiased view of both the genotypes compared to one control.

btw, never heard of a miRNA array in dual color..Guess exiqon is the only one offering that!

gogreen on Dec 14 2009, 01:01 PM said:

thanks for your comment
I might think about a single color as well, that's a good idea. But Exiqon recommends a dual color with reference design for they arrays. I have to figure.
And one more question, do you know is the TM4 suite is capable of handling the reference design data?
As for the arrays, yes, both Exiqon and Invitrogen are offering microRNA microarray with dual-color labeling kits.

k

kaveh on Dec 15 2009, 02:51 AM said:

sorry , No clue about the TM4 suite..