I have to perform Western Blot on FFPE tissue and the first part is the extraction.

First I did deparaffination, then I added the extraction buffer (20 mM Tris-HCl pH 8, 2% SDS) and I incubated for 20 minutes at 99°C and for 2h at 80°C.

This is the result with and without pellet. Can I understand by eye if the proteins are in here? Is there some clue that makes me understand that the lysis didn't occur correctly? Or do I have to wait until staining with ponceau S?

Someone that did something similar could tell me if this is the right apperance?

Thanks for your help

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