Hi all,
Is it possible to extract RNA from formalin fixed paraffin embedded tissue sections which would be good enough in quality and quantity for RNA sequencing?
I have some slides with mouse lung tumours and would like to check if I can extract RNA from the sections on slides.
Thank you,
Vrushali
Good morning Vrushali,
It certainly is possible, but it can be a bit of a pain. There are several kits available on market that you can use to do the extraction. We have used kits from MoBio, Qiagen and Promega. These different kits resulted in different yields from various tissue types. We noticed a significant difference in final RNA yield from various tissue types - from some tissues we could just not get enough material.
I would suggest you use some kind of rRNA depletion protocol instead of mRNA capture as the RNA will be degraded and you will struggle to get enough material using a capture based method. Try to aim for a higher input amount to give yourself the best chance at success. If you have some spare time, have a look at this presentation on low quality RNA samples: https://vimeo.com/207154511
You can then analyze the extracted RNA on a BioAnalyzer and get an idea of the quality from the RIN or DV200 score but the ultimate test of the quality of RNA will come when you construct the library. The only advice I can give here is to try and go in with enough template that you are clear of any lower limits set by the kit of choice. Have a look at different kits before hand, unless you already decided on one, and make sure that they are compatible with FFPE extracted RNA. Some manufactures will state very clearly that their kits are not for use with degraded RNA samples.
Let me know if you have any specific questions.
Best of luck!
Chris