We do a lot of measurements using the microarray setting on the nanodrop. It is mainly to establish the amount of dye incorporated into our created cRNA. Now the issue that we are having is that the baseline (the black line on the bottom) moves up quite drastically and more or less randomly. It usually means we have to re-measure every sample 3-4 times with blanks in between to get the baseline to stay at 0. The values for the dye and amount of RNA change quite a bit when the baseline is not at 0 and so we try to get a measurement where the baseline is where it is meant to be.
It gets quite tedious when measuring >24 samples at a time as you can spend hours at the nanodrop trying to get good readings.
Does anyone have an explanation as to why this happens?
Does anyone know how to avoid that?
Friend of mine who works for biotech equipment distributor had experience with Picodrop (very similar system) and many people had problems similar to yours. She thinks it is hardware issue, so not much you can do about it.
On the other hand, you can try contact distributor/manufacturer and ask for support - they may send you new unit if you manage to prove that device itself is faulty.
Try using low lint tissue paper for wiping off your sample stage. We switched to this a year or so ago and it has alleviated almost all "bounce" on our readings.
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