Having run and analyzed a few thousand RNA samples on the Fragment Analyzer I have, in rare occasion, observed samples with no 28S peak in perfectly intact RNA. The samples are not from insects or crustacean, they are from mammalians, plants, fish.
The obvious cases (intact RNA and no 28S) are easy to catch and the wrong low RQN can just be ignored.
However, it becomes a nightmare when the 28S is missing and some partial degradation is also observed. The RQN is wrong and there is no ways to estimate a reasonable RQN value.
Now interesting is that if the same samples, same plate, same lane is run again a few hours later the 28S can appear or disappear. ?!? The only changes are the conditioning and gel injection in the capillaries. Nothing else has changed.
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