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gavin.oliver 03-02-2010 06:23 AM

RNA-Seq from FFPE Samples
Hi all,

Just wondering if anyone knows anything about doing this?

I read an article by Beck et al where they developed a method called 3SEQ for RNA-Seq from FFPE samples (using the Illumina GA) but this method concentrates only on the extreme 3` end of samples and therefore obviously misses out on a lot of upstream information.

I have read that single molecule sequencing is most suited to profiling mRNA from degraded samples and I am wondering if the Helicos or Pacific Bio machines would be suited to such analyses? Or will their techniques be 3`-biased also?

Any feedback would be greatly appreciated



SallyH 04-27-2012 04:52 AM


I know this post was a long time ago, but did you do any RNA Seq from FFPE samples? If so which sample prep method did you use please? I am trying to decide between DSN normalization or the mRNA-Seq Sample Preparation kit (if I can get enough total RNA from the FFPE samples).

gavin.oliver 04-30-2012 12:14 AM


The project fell by the wayside in the end unfortunately.

I heard numerous claims that DSN normalization works very well but only in the right hands - it seems to be a temperamental protocol.

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