You can search for commercially available kits like Qiagen Total RNA kit . But I am really not sure whether the Formalin was able to prevent RNA degradation during the preservation period, as it is a good preservative for cells. Try to preserve cells in RNA Later, as it gives good results even after months long preservation.

Good luck.

Thank you Zainab,

Indeed RNA later or frozen tissue is a better choice but imagine how many information could be available in old samples fixed and embedded.

Formalin induce a certain degree of RNA degradation, in specific it creates RNA–protein crosslinking. In general it is possible to recover a certain amount of RNA from FFPE tissue, although heavily fragmented. 

 Since there are many kits that can help in this process I would like to know if someone has tried this technique before and can give me some advice.

Many thanks

If you are planning to do RNA-seq, I suggest you to use AllPrep DNA/RNA FFPE extraction kit from Qiagen (code #80234). It works pretty well (altough the quality of RNA is not comparable to the one from fresh tissues/cells). With this kit, you can also isolate DNA for other analyses as well. 

Contact the VSU at Moredun, they do this all the time from 2 x 10 micrometer slices we cut them, using gloves!, and placed into eppendorfs.

Yours,

Mark

Thank you Mark!

VSU contacted.

We have had generated quality data using Affymetrix miR arrays, RNA-seq and exome-captured NGS from RNA and DNA using the Recoverall Kit from Ambion/Life Technoloiges.  4-8 10micron curls (pooled then processed) were initially taken and the kit instructions were followed as recommended. 

We have also successfully used a 1mm punch-biopsy device to sample tumor and normal regions from FFPE blocks.  An overnight incubation is necessary to completely digest the material .  Separate aliquots of the digested material may be processed to isolate the nucleic acid fractions of interest.

Hello,

I'm from Promega and worked on an FFPE RNA purification kit. If you have access to a Maxwell instrument you can use our Maxwell FFPE RNA kit. I regularly purified RNA from 5 micron mouse skin sections that were 17mmx 1mm.

FFPE kit from Qiagen works well but for the yield you need to digest at least overnight, better 48 h with 10 ul PK boost after first 24 h. I also add RNAse inhibitor for the PK digest step.

Yelena