I am extracting DNA and RNA from FFPE tissue, matched colorectal metastasis, primary tumour and matched normal tissue. (RNA is complete, with the DNA I am going on to do exome sequencing and methylation arrays.)

I have used the Covaris truXTRAC® FFPE DNA and RNA Kits, some samples were low concentration (I am aiming for 300ng/50ul) and so I repeated them, and then again for those that were still low with the Covaris truXTRAC® FFPE DNA kit.

I have noticed there is a greater proportion of normal tissue which is of low contraction (10 samples vs. 4) and wondered if this is because it is mainly adipose tissue e.g. omentum?

I wonder if anyone has any experience / can recommend a different extraction method to maximise the yield from this tissue? (FFPE, adipose tissue)

Many thanks,

Sally

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