Hi everyone. i've sent RNA samples for sequenicing. when checking in nano-drop the 260/280 ratio was great (2-2.1) but in some samples the 260/230 ratio was around 1.7-1.8. by running the samples on agarose gel the gel was great. would the sequencing be good enough even though i had lower 260/230 ratio?
thanks
260/230 is (typically) a check for guanidium salt contamination: a chaotropic salt used in many RNA isolation protocols. As a chaotropic salt, it can interfere with a lot of downstream reactions.
Ideally this ratio should be 2.0 or above, but I would usually consider a 260/230 of 1.8 to be pretty good, certainly for most standard enzyme-based downstream procedures. 1.7 is my preferred minimum for cDNA synthesis, for example.
A cursory scan of the internet suggests there is no hard-and-fast lower limit, and some enzymes will tolerate higher salt contamination than others, so since you've already sent off the sample, I suggest you simply make a note of this, and then wait and see.
If you have good 260/280 value and moderate 260/230 value it should bear not much of a problem with RNA-Seq, many companies consider a value above 1.5 for 260/230 fit for sequencing. I support the view of others, you can proceed with your samples for sequencing.
Best Wishes
Pankaj
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