I am trying to optimize the ChIP process, which I would be later sending for sequencing. But before sending the samples for sequencing, I wanted to check for the presence of known DNA. So, I was planning of performing a qPCR but I am not sure of what DNA are used for making the qPCR standard?
Is it the input DNA sample? or isolate the total genomic DNA?
Genomic DNA can be used, but the most common method I've seen is inserting the target sequence into a plasmid.
You can do this on you own via cloning. I've had success using the TOPO TA Cloning kit from Life Technologies. https://www.lifetechnologies.com/us/en/home/life-science/cloning/topo/topo-ta-cloning.html
Am even easier method is having a plasmid standard synthesized. Genewiz offers this service at a good price and sequencing is included with the synthesis service http://www.genewiz.com/public/gene-synthesis.aspx
I don't see why genomic DNA that is very clean and high molecular weight would not serve as an adequate standard. You can measure the A260, calculate the concentration and then calculate the specific concentration of the segment you are going to amplify based on its size and the size of the genome. Linear genomic DNA might also be a more comparable template to the target you are measuring than closed circular plasmid.
If you want to know if the ChIP actually worked or not, then the approach you might take is to do a parallel ChIP with a non-specific antibody (this is often called the "IGG control"). Then compare qPCR results of this control with your specific antibody pull-down.
Input DNA is the most common standard in ChIP-qPCR. If you look at figures on literatures, they always normalize their data to percent of input. But in your case, you just want to check your ChIP work or not, then you don't need standard indeed. As David said, comparing the enrichment of targeting Ab to IgG control is enough.
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