I am performing a ChIP protocol to study an histone H3 post-translational modification in cancer, using as initial samples FFPE tissues.

I'm using the iDeal ChIP-FFPE Kit from Diagenode (C01010190). However, after taking INPUT aliquots from the chromatin pool before the sonication step and after each round of sonication (3 total rounds), and after doing a western blot, I wasn't able to detect any band for my histone modification in any of the INPUTs. The protein quantification (using the Bradford assay) of the chromatin pool gave me a concentration of approx 2 ug/ul, for approx 1000 ug of proteins.

My question is: could the extraction have been inefficient, resulting in the complete loss of my histone modification from the chromatin pool? I followed the extraction protocol described in the kit, with resuspension in lysis buffer, followed by homogenization with Douncer homogenizer and incubation for 1h30 at 65°C for antigen retrieval. The INPUTs were eluted with a solution containing beta-mercaptoethanol for 25 min at 95°C before loading onto a Precast 4-12% SDS-PAGE gel.