We are doing ChIP-chip experiment on plant materials, the problem is that we could not amplify the ChIPed DNA with WGA kit.
We followed the published protocol for ChIP: http://www.ncbi.nlm....ubmed/15315638.
Generally, we harvested 4g plant leaf tissue and corsslinked it in 1% formaldehyde for 5 minutes and stop reaction for 5 minutes in a vacuum.
After the sonication step, we did aliquot some sample and let it go through the reverse crosslink procedure. The fragment size is well between 200bp to 1kb.
After the ChIP step, we got about 500ng total DNA. When use 20-30ng for PCR, we got good results with positive and negative controls, which are known for being ChIPed or not.
However, we then shipped our sample to company for microarray. The sample could not be amplified with WGA kit following standard procedures.
Does anyone encounter similar problems?
Cannot make a library from the ChIPed DNA
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