I am trying to standardize ChIP in my lab.. but unable to do that, I have tried with different protocols, but all failed. So I am asking is there any way to calculate the amount of DNA?
This step is unnecessary, as you will normalize your ChIPed DNA with the input DNA.
But if you want to calculate ChIPed DNA (usually for library preparation for ChIP-seq), you can use qubit/denovix dsDNA HS quantification method.
Hendry Susila
thank you so much for your answer, but is there any way to know the initial amount chromatin I am using before addition of Antibody? or is the amount of antibody added depends on chromatin concentration?
You can quantify the total DNA after nuclear lysis, although it's not necessary. I usually use similar amount of starting material for my sample.
Well, the amount of antibody should be correlated with the amount of your protein of interest, for instance, histone vs TF.
thank you again. my protein of interest is histone H3. can you suggest the protein concentration and antibody? for what concentration of protein how much antibody is required? Hendry Susila
It depends on your sample (plant/animal tissue/cells). Several previous publications probably use similar samples and histone targets like you.
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