Has anyone had luck with NGS library prep for DNA/RNA samples that had low A260/230 ratio due to guanidine thiocyanate? Our samples are made using the AllPrep Qiagen kit without Trizol (used other lysis buffer) and phenol precipitation does not help much. NB, phenol is not the issue.
Thanks.
If you use a poor quality sample, you should expect poor quality results, unreliable results, and/or unrepeatable results. I would recommend against using a sample with organic contamination.
Craig Silver, thanks for your generic comment. However, I asked about particular experience people may have had with low A260/230 values. I understand you have not had any issues because you always use highest quality samples. Good for you.
The contaminants inhibit and interfere with PCR reactions, (primer annealing, polymerase activity, kinetics, etc). If you want to use a sample you know is bad, by all means, go for it. Your data won't be publishable, no journal would permit conclusions drawn from samples you just said you know are bad.
Good luck.
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