I need a very good quality RNA for RNA-Seq. When I run the RNA on 1% agarose gel the sample looks good. But the same sample on Bioanalyzer shows a low RIN value. Which method is more reliable to check the quality of RNA - gel or bioanalyzer?
Hi,
Bioanalyzer should perform better than agarose gel. The RIN is a good indicator, and most sequencing platform require samples to have a RIN above a certain threshold for further processing (I guess every platform has is own standards, but for example RIN > 8.5 for eukaryote's tissues). Nevertheless, beyond the RIN the profile of the electropherogram for each sample is the best indicator. And the software normally also reconstitute a gel that can be informative as well.
So even with a good agarose gel, I would rather trust the indications from the bioanalyzer.
Best,
I will probably believe in Bioanalyzer results rather than the gel. I usually recommend RNA for RNA-sequencing to have its RIN of at least 8 - i recalled Illumina also said so in their protocol, but the higher the better obviously. However depend on your species, sometimes it does not have a RIN number, or a weird RIN value. For instance, if you extract RNA from prawn/lobster, it usually have a low RIN (5,6..) or even doesn't have a RIN recored at all.
Hope this help,
Are you sure you're gel is good? Can you show it to us? Depending on a species, low RIN number doesn't necessarily mean you have bad RNA
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