The preparation of the chromatin requires some optimizations. Like a treatment with lyzozyme to help lysate of the membrane. Here is attached a publication and we also have some ChIP kits that could help you at Diagenode.

https://www.diagenode.com/

Article Response Regulator Heterodimer Formation Controls a Key Stag...

Hi, It's best to use nitrogen grinding in mortar and pestle to make the lysate. Use 50 mM Tris pH 8 and also use 150-200 mM Nacl. add 500 ul of lysis buffer to the morter and grind the frozen pellet with the buffer. Once you get the lysate add protease inhibitor to 1 x and triton 0.8%. Final volume should be 1250 ul total in a 1.5 ml tube. then sonicate 20 times 1/2 power 15 sec on 45 sec off. You should almost clear lysate after sonication. That should suffice. When you check DNA size, butter to use bioanalyzer/tapestation.. If you don't have it, then run a gel after 2 phenol:chlorform extractions followed by rnase treatment 10 mins followed by another phenol : Chl extraction and then finally Chloroform extraction to remove the residual phenol. take 25 ul of DNA and run it on ge. You should see a smear from 1000 to 200 and averaging at about 300-400. Remember that your DNA is crosslinked to protein so it will be ~100 bp slower than the control (over estimated). I hope that helps. Good luck.. 

Hello Mahmoud,

Thank you for the comprehensive answer. I will try my best.

Best regards,

Sudip

Hi Sudip Das ,

I stumbled upon this query of yours while looking for chip-seq data of microbials.

were you able to generate chip reads for staphylococcus? If yes, Is this data available publicly?

Any advice is highly appreciate .