I am doing ChIP experiment and get very strange result. Since I'm new to this field, I am curious if it's normal or something's wrong,
In my experiment, I'm ChIPing five candidate gene sites with my transcriptional factor. I did PCR for these five genes. For three of them, I got strong enrichment for my ChIP DNA sample, but the NO-AB controls have also strong bands similar to INPUT. However, no bands was found in NO-AB controls for another two genes, although one ChIP DNA sample has band and the other has no signal.
The only suspect I can think of is the non-specific affinity in No-AB control. I hypothesis that the chromatin fragment has randomly affinitied to Protein A in No-AB sample. If the target genes we interested were among them, it resulted in signals in NO-AB sample; but if the target genes were not included, no signals were found.Is it?
I wonder if my explanation is reasonable
.Can anyone help me to explain this result? And how can I avoid this unexpected result?
Any help would be highly appreciated.
Thanks in advance
Chip Helps - Why Strong PCR signal from No-AB control sample
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