I am extracting RNA from FFPE tissue (Phenol Chloroform method). I am not being able to achieve complete homogenization with the tissue homogenizer. I was thinking about using sonication. Do you recommend this method? Does it affect the RNA integrity and stability if it'll be used for cDNA synthesis?
Do you suggest any other method?
Hi Emile,
For the last year I have had a hard time extracting intact RNA with bead beating (the cells I work with are armored algae and hence hard to open). The bead beating (which I think is similar to homogenization) caused either incomplete cell disruption or totally trashed the RNA, leaving degraded extracts. I'd go with David's answer on sonication, as it's not something I am familiar with.
Though I've found a different method for harvesting that works well for me - freeze thaw. Once my samples are in Trizol (also phenol chloroform) I place them in liquid nitrogen till completely frozen, then onto a 95 degree heat block till thawed.
This method may work for you too.
All the best!
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