I am trying to do qPCR from lung tissue in OCT. The whole lungs are inflated with cryomatrix for the histology purpose, so there's no way of peeling the cryomatrix off. My question is - does anyone have experience, does cryomatrix affect PCR? Or does it affect RNA extraction (Trizol)? I could of course make a test run w/o cryomatrix, but if anyone has any experience about the potential influence, would very much appreciate.
It is well known that OCT interferes with RNA isolation. It is not possible to get rid of it completely from lung tissue as you stated. Therefore we use surgical string to tie one of the lung lobes before injecting OCT into airways and snap freeze this OCT free lobe for RNA isolation.
Please read the first link, there John Hildyard has highlighted major points to avoid OCT problems, in case you have to work with already prepared lung specimens.
https://www.researchgate.net/post/Ways_to_extract_RNA_from_OCT_optimal_cutting_temperature_compound_embedded_tissues
https://www.researchgate.net/post/How_can_i_make_RNA_extraction_from_frozen_tissue_in_OCT_to_develop_qRT-PCR
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