RNA quality for microarray - What must be the ratios? (Apr/27/2007 )

Hi, there!
I am working with AD patients lymphocytes and I am preparing RNA samples for microarray method.
I have been reading articles and some protocols, and they only mention 260/280 ratio, which must be >1.6. However, in none of them it is cited the 260/230 ratio.
My question are: (1) is the 260/230 ratio as important as the 260/280?; (2) what must be its value for a good RNA quality for microarray; and (3) what can I do to increase this ratio?
Please, could you help me?

Doda

Hi Doda,
I worked with bacterial RNA for the affy chip microarray quite recently. I think ratio of A260/A280 is more important in terms of indication of free of protein contanimation, if the ratio is more than 1.8. And if my memory was correct, the ratio of A260/A230 is indication of contamination of organic solvant? (I am not sure of this, please check), but I am not usually bothered too much by this ratio..

I think, if the ratio of A260/A280 falls in between 1.60-2.00, it should be fine. And I use Qiagen RNAeasy kit for the RNA extraction. One thing I always do after the extraction is to check the RNA quality (integrity) by running 1ul of RNA sample into a RNA nanochip (Agilent Bioanlyzer 2100)...As long as the running result shows no RNA degration, I would be confident in the quality and go on with the cDNA synthesis and etc.

hope this helps..

cheers,

VF

according to sambrook 260/280= 1.8 to 2.0 is good quality rna
we use same value for real time pcr

Hi, VFinMadison!

About my A260/280 ratios, I think they are fine! My concern was about the A260/230 ratios, which are not OK (0.4-0.7 the worst ones). And yes, this ratio indicates organic solvent contamination.
So, do you think if I keep my A260/280 ratio between 1.6-2.0 is it Ok to use them for microarray?
Thanks for your reply.

Doda

Hi, LDW!

What about A260/230, how much can it affect for microarray? Is it just fine to work with a sample with A260/230 ratio between 0.3-0.7?
Thanks.

Doda.