I've done a few ChIPs so far for eventual sequencing and I've finally gotten through one where I don't remember making any obvious mistakes.
I mostly follow these protocols
https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1365-313X.2004.02169.x
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3952383/
when I purify and test the pulled down DNA I'm getting about 5.68ng/40uL for my experimental treatment and 4 to
Hi!
I recommend you to analyze the input fraction to test your primers. And the second one: try to use pcr product from the first round of pcr as a template for the second round with the same primers.
If you planing to do NGS sequencing, this amount of DNA is sufficient.
1) I don't think it is an obvious failure, Antibodies are sticky and they bind to other stuff as well. Mere amount of DNA ChIPed won't say if a ChIP worked or not
2) The low yield could be because of low antibody addition, make sure you add enough antibody and also try doing the indirect method for the actual ChIP.
I made a presentation to optimize ChIP, Hope that helps.
Diagenode has a specific kit for ChIP-seq on plant validated on Arabidopsis and different tissue.
https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns
Also make sure you have high quality antibodies validated in ChIP-seq. Diagenode has also very high quality and tested on Arabidopsis for most of the histone marks
https://www.diagenode.com/en/categories/all-antibodies
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