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Old 11-22-2017, 09:38 AM   #1
Elugop
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Question RNA integrity number Drosophila

Hello @all
as we want to start an RNA-Seq analysis we try to determine the quality of our RNA (Drosophila heads) first. When we did this via Bioanalyzer an error occurred as expected. The measurement in a TapeStation results in a RIN though. I can`t explain why because still no 28S peak is visible. The RIN is the ration of 28S to 18S as I understood this.
Therefore I don`t know if I can rely on that. Does someone have experience with that?
Thank you!
Jule

ps: attached you see the trace of one sample with both machines
Attached Images
File Type: png Drosophila RNA_Bioanalyzer_9.png (68.9 KB, 12 views)
File Type: png DrosophilaRNA_TapeStation_9.png (92.5 KB, 11 views)
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Old 11-22-2017, 11:50 AM   #2
ericchow
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It's a result of the 28S from insects being split. See this article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3016993/
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Old 11-22-2017, 06:44 PM   #3
luc
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As consequence from what Eric wrote, one often has to eyeball the RNA integrity for insect samples on the Bioanalyzer (I am looking ratio of the rRNA peak size to the smaller debris fragments).
Your example trace looks great.
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Old 11-27-2017, 05:41 AM   #4
Elugop
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Thanks - I try it with these samples now. Fingers crossed
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Old 11-27-2017, 09:02 AM   #5
HarbsSM
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Hi,
I'd suggest using the Bioanalyzer over the Tapestation in the future. It gives a more granular electropherogram, whereas the Tapestation directly images the gel image from the run. This results in a less detailed electropherogram. Your trace looks good, but the RIN/RINe values are effectively redundant for insect material. Eyes are the best measure.

The link above is a great explanation!
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