Another easy to execute denaturing gel that will give you good resolution is a "bleach gel". They are extremely easy to prepare and they also have the advantage of inactivating RNases, meaning no pre-treatment with DEPC. I have used them many times to evaluate RNA quality. Any household brand of bleach should work (~5% sodium hypochlorite). I have included the protocol publication linked below.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3699176/

If you want the RNA to run true to size, you have to use a denaturant, otherwise the RNA will run partially folded.  I have used glyoxal agarose gels, RNA chips on the original BioAnalyzer, and on the AATI high-throughput machines. BTW, my experience is that you have to keep the equipment (agarose, tank, pipettors, AATI capillary array, etc) dedicated to RNA work or no matter how much you use RNAse Away and DEPC,  RNAse will kill your most valuable RNA.

Leila hi!!, I have worked with 3ug of total RNA and have prepared 50ml of 1% agarose, with 0,75gr Agarose, 1 mL TAE (50X) and 49mL of deionized water. For this amount 1uL or 0.8ul of ethidium bromide is excellent. I think that this amount also depends of how much amount of gel you will prepare. A similar concentration, even a little less, can work. I run the electrophoresis with 80-100 voltage for 15 minutes, although these values also depends of the size of the box you use. For me, it has worked very well in RNA extractions monocots flowers with Trizol. Regards! :)

Thanks Yesenia Madrigal and Ann Holtz-Morris, for your help I appreciate this.

Regards.

What do you need to see in your gel?

I made successful RNA electrophoresis of RNA probes for ISH on agarose gels with the same etbr concentration used for DNA. To avoid RNA folding heat 95ºC for 5 min and then cool down on ice for a few minutes before running it. Everything needs to be DEPC treated, if you do not have a dedicated tank you should clean the one you will use very well just before running your gel.

Good luck!

Another easy to execute denaturing gel that will give you good resolution is a "bleach gel". They are extremely easy to prepare and they also have the advantage of inactivating RNases, meaning no pre-treatment with DEPC. I have used them many times to evaluate RNA quality. Any household brand of bleach should work (~5% sodium hypochlorite). I have included the protocol publication linked below.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3699176/

 Thanks Jordan Tan Pepper for this paper,

I will try using the bleach gel as you recommend and will let u know the results.

Its easy and very available, so I will give it a trial; i will do it as follwoing

0,5gr Agarose, 1 mL TAE (50X) and 46.5mL of deionized water + 2.5 ml Clorox

Regards.

Hi Leila, I think 2.5 ml of clorox is too much. 0.5 ml should do the work, take a look at Table 1 of Bleach Gel: A Simple Agarose Gel for Analyzing RNA Quality

Hi Andrius,

could you tell me how can I measure that RNA band size? and how many bands I should have from after RNA isolation from eukaryote cell ??

 Hi Zinad,

if you want to get approx. band size you can run agarose gel + RNA size marker/ladders. And in most cases there will be 2 clearly visible 28S and 18S rRNA bands (assuming your RNA sample is not degraded).

Thank you Andrius...