mRNA samples used for microarray, we normally check for RIN(>7) and quantity same as you do, apart from this we also check for A260/230 (1.8-2.1) and A260/280 (1.9-2.1) ratios by nanodrop.

Hi Priyanka,

Thanks for the reply. I have some samples whose RIN is above 8 but the A260/A230 ratios are in the range of 0.7-1.6 . Do you think the samples are still ok to be sent to microarray??

It depends on wat method u have used for extraction. eg if u use Tizol normally u will get ratio in this range but still it would be better if u get it confirmed. I use QAIGEN coloumns and use RNA only if ratio is more than 1.9 or else its not accepted, due to problem in labelling and all. So get it confirmed before u send.

My experience is that the 260/230 may or may not influence your microarray results, depending on what extraction method was used, and what microarray platform you will use. I suggest you ask the microarray lab if thay have any experience with low ratio samples extracted with the same kits as you use, and how these samples perform in the microarray analysis (present calls, expression profile differences etc).

Good luck.

i used trizol method to extract both mRNA and miRNAs....i will confirm the microarray centre regarding these ratios. Thanks for the answers

using Trizol for small RNA isolation may not be the most appropriate method (see Kim, et al. (29 Jun 2012) Molecular Cell, Vol 46, Issue 6. "Short Structured RNAs with Low GC Content are Selectively Lost During Extraction from a Small Number of Cells"). miRvana (as cited by the authors) may provide a better and more reliable protocol and set of reagents for small RNA isolation.

We considered this article before proceeding to the extraction. The method which we use is different from what they have used in the paper. we also checked our small RNAs using bioanalyzer and i can say that the results are promising till now.

I don't think bioanalyzer analysis can say anything about what the Narry Kim's paper is talking about