For recovery of the immunoprecipitated DNA, can I get better results with a phenol chloroform extraction instead of a column extraction?
The efficiency and yield of the DNA extraction is typically higher using a phenol chloroform extraction. However, same people still use column extraction to get the DNA for downstream applications such as PCR or T7 amplification for microarray (ChIP-chip) analysis. Also on this way our kit was validated for microarray analysis. Pooling multiple samples prior to DNA purification may improve yields for column extractions.