Hi all--
I'm preparing plant root samples for RNAseq and have been investigating some samples that had suspicious bands in their lanes when I ran a 1% non-denaturing RNA QC gel. To spot check some things, I ran some of my worst and best looking samples on our TapeStation to see what RIN it would spit out. This sample is one of the better ones and has an acceptable RIN value-- but, for some reason that algorithm isn't detecting the upper peak and has labeled it as 18S.
Does anyone know why this happens? Is this a consequence of the smaller (organelle?) peak just after it or because my samples are plants and non mammalian? Or something else entirely....
Further, does anyone know if this will affect the RIN score calculation?
Any suggestions, feedback, or wisdom would be much appreciated. I've attached an example of the unlabeled peak and the gel with my mix of good and bad samples.
Thank you!
It appears that the algorithm is looking for a mammalian 28S peak instead of a plant 25S. As a result, the peaks are integrated incorrectly. This can be manually corrected in the Tapestation analysis software.
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