I'm hoping someone might be able to answer something that has been confusing me lately.
Basically, I have harvested a lot of RNA from iMR90 and U2OS cells over the last two or three months using Trizol extraction, which I then clean up using a Qiagen RNeasy mini kit.
My problem is, that for one particular experiment, all of the RNA I get seems to have a low A260/230 ratio on the nanodrop which I've heard is a result of phenol contamination or some other contaminant. The problem is, that when I clean up RNA from several experiments together, it's only ever this one experiment which gives low A260/230 ratios so it's not likely a problem caused during the clean up.
The only thing I can think of that is different is that these samples had been isolated in Trizol, and then stored at -80oC for a few weeks longer than the rest.
Would this cause this kind of absorbance value? I'm not doing microarrays with the RNA and I don't seem to have a problem with making cDNA for q-PCR so it's more of a curiosity than a burning issue I need resolved. Any input or advice would definitely be appreciated though!
Thanks in advance for your help/opinions,
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