please! help on DNase treatment before microarray of RNA, which one?! - (Dec/10/2008 )

Hello,

I am trying to prepare samples for microarray, I extract my RNA with a decent amount but need to do the DNase treatment. I am using RQ1 RNase-Free DNase treatment "twice", the thing i see for a few samples were:

very low, RNA or DNA or
(generally this one) high RNA and DNA with good quality when i check with Nanodrop.

So, it treats everything or does not treat anything(mostly) or I really could not optimize my protocol.

So would you please tell me any other efficient DNase treatment that I can use?

Thanks

Did you try DNAse from another lab? Maybe yours is bad

thank you for replying...

Actually i did not, so I guess need to get a new one. I am really not experienced on these, do you have any recommendations on the kit I could use for DNase treatment, practical and efficient?

I don't know if there are DNase kits out there. You just buy the DNAse from a company and it will probably also come with a buffer.
This is part of our protocol that we use for the DNAse treatment of isolated RNA:

8. Suspend RNA in 90 ul RNase free water (don’t suspend in DNaseI buffer), may need to heat 5-10 min at 55-60C to dissolve RNA. (oprional: obtain RNA concentration)
9. Add 10µl 10X DNaseI buffer to RNA (use no more than 80 µg RNA) and add 2µl DNaseI. Incubate 30m at 37C.

Then we use the Qiagen RNeasy purification kits to clean and concentrate the RNA.