For my thesis I am isolating RNA from Fusarium infected tulip bulbs to study a certain gen expression. I am using the Qiagen RNeasy Plant Mini Kit for isolating the RNA. The kit comes with RNase free water to store the RNA in. However, when I run the samples on a gel (EtBr, 45 min at 60V) the RNA seems a bit degraded. What can I do to prevent this?
Hello Marlies!
There are so many factors in your RNA degradation that might not be only due to the isolations steps:
-every material in contact with RNA should be Rnase free, tips, water, even gloves, there are solutions where you can prepare and most soak of the lab material in order to make them RNAse free.
-Agarose gel stained with EtBr is not a good choice for preserving RNA during the electrophoresis, if you dont have the sources for special gels , I recomend you to use the Bleach-gel variation (Aranda et al. 2012) which has given excellent results to me. https://www.ncbi.nlm.nih.gov/pubmed/22222980
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