RNA-seq for samples with RIN<3

Question

[mariam28071993]

Hello,

I have sent a few total RNA samples for RNA-seq (100 M reads, 100PE, rRNA depletion, DNBseq). However, the bioanalyzer results came back as unqualified because of RNA degradation and a RIN of 2.5-2.8. Is there any way I can proceed with the library preparation, or it's impossible that the sequencing will produce sufficient data?

Thank you very much for your time :)

[svl]

Did you sequence these in the end? Interested to hear wha sort of results you got if so. I have a similar issue with low RIN from some hard to come by samples..

[Emilie]

Also in this boat and am curious!

Answer 1

[karl.stamm]

What does a low RIN mean? My understanding is it's a measure of the RNA 'quality' in the sense of degradation and the ratio of full length molecules vs broken-down components.

Would NOT recommend spending any resources on sequencing it. You will get 'some' results from sequencing, but it will not be comparable to public or previously run controls.

Unless of course that degredation is part of your experiment; you want to see which mRNA survived the sample handling.

[mariam28071993]

The problem is that these samples include controls. And, the purpose of the sequencing was to analyze the whole transcriptome of total RNA extracted from very rare and "hard to come across" samples, no degradation or sonication was carried out after extraction. Of course, the sequencing company's advice is not to proceed with the sequencing, but I don't have other samples to send and I think in this case my whole project would be terminated.

Thank you so much for sharing your opinion, I appreciate it.