Hi Dear all,
I am focusing on ChIP now. A key point is that how to design a primer of gene promoter, that is the sequencing binding regulatory element factor. Thank you so much and appreciate it.
Shiqiao
Hi,
You need to identify possible binding sites for your factor in the promoter region - you can do this by eye, or use a motif search tool such as http://motifmap.ics.uci.edu/
When you have a potential binding site design primers 50-100bp upstream and downstream from this so your potential binding site is in the centre and you get a fragment size between 100-200bp. If you have more than 1 site you can incorporate them into the same fragment, or design 2 sets of primers to isolate them - the latter approach will allow you to identify which (or both) bind to your ChiPed protein / mark.
Hope this helps
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