One of my colleague thinks that the RNA quality should be fine for those cryo-sliced liver tumor samples. We just need to use more sliced samples to get enough RNA. Is this correct?
I would recommend running some of the RNA on an Agilent Bioanalyzer. In addition to RNA yield, it will provide a RNA Integrity Number (RIN) which will determine if the RNA is of sufficient quality/yield for sequencing. Your sequencing protocol should describe RIN quality required. If you don't have access to a Bioanalyzer, run some RNA on an agarose gel and judge the appearance of 28S, 18S and 5S rRNA bands as an indication of RNA quality. As the samples are FF, they should be fine, better than FFPE-derived RNA.
I would recommend running some of the RNA on an Agilent Bioanalyzer. In addition to RNA yield, it will provide a RNA Integrity Number (RIN) which will determine if the RNA is of sufficient quality/yield for sequencing. Your sequencing protocol should describe RIN quality required. If you don't have access to a Bioanalyzer, run some RNA on an agarose gel and judge the appearance of 28S, 18S and 5S rRNA bands as an indication of RNA quality. As the samples are FF, they should be fine, better than FFPE-derived RNA.
With 5-8 year old FFPE samples, I would expect significant RNA degradation, cross-linking, etc. However, frozen samples usually maintain nucleic acid integrity much better. Hopefully you get decent RIN results from the Bioanalyzer analysis.
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