In addition to Alice's suggestions you could also take an aliquot of your sonicated and non-sonicated chromatin  perform de-crosslinking proteinase K and RNaseA as stated in your protocol run in a gel without cleaning your DNA. Just to check the sonication. 

You could try two or 3 different dilutions of your de-crosslinked chromatin in the gel. 

Best wishes, 

Adriana

How much DNA do you expect to see in your sample.  I have no idea how may nuclei are in the starting material, but you may have very few.  The band you see may be ribosomal RNA, which is why it disappears after treatment. 

ohhh, before isolating your chromatin you should ensure that you have more than 5 million cells as starting material. 

Hi Haque,

Another suggestion about sonication:

I see that you use 90% power. Even though you hit the cells for 20sec, 90% power would generate a lot of heat which can denature the DNA. I would not go beyond 50-60% power and try conditions like 30sec On, 30 Sec Off. Collect aliquots after every 5 cycles upto a total of 30 cycles. Keep un-sonicated sample as control. 

After you collect the aliquots, as suggested by Adriana, carry-out reverse crosslinking using Sodium Chloride at 65C Overnight in a Thermomixer. The, RNase A digestion 37C/2Hours, Proteinase K 55C/2Hours, Phenol"Chloroform extraction followed by EtOH precipitation (use Glycogen). Resuspend pellet in water, measure concentration by Nanodrop ad load on 2% Gel . If everything goes well, you should see what you expect to see.

I am attaching an image for you to show the outcome of what I got by following the procedure described by me. 

Hope this helps. Good Luck!

Utkarsh