If your sample is not crosslinked, you can go ahead and directly extract DNA from the sample using a Qiagen PCR purification kit (they have a modification that you can add 5 volumes of the Binding Buffer (PG?) to the nucleosome-DNA solution and then bind it to the column - wash with PE once or twice and then elute with TE or just Tris or Sterile MilliQ water. 

However if your sample is crosslinked as usualy ChIP samples are - after elution, then decrosslink the sample with 1% SDS at 65degC for 2-4 hr and then dilute to 2 volumes using autoclaved water, and then proceed with adding 5 volumes of the binding buffer (Consider 1X volume as per final volume with water+SDS). 

Samples purified this way are good for PCR as well as Whole genome amplification and sequencing. If you do not have this Kit, u can use any other manufacturer's kit that is for small DNA fragments. However if you do not have any access to DNA purification kits, you can still try to extract sample with freshly equilibriated Phenol:Chloroform:Isoamylalchohol once followed by Chloroform extraction, then precipitation of nucleic acids with 0.3M NaAcetate and 2 volumes of 100% ethanol. Wash precipitate with 70% Ethanol - air dry it - and resuspend in TE for analysis. 

Thank you all for the inputs. I tried Phenol Chloroform extraction followed by Ethanol precipitation as described by Subhojit and Ali, and looks like it is working fine in my case. Thanks again.