What are your samples? I.e. cell culture or primary tissue? As far as tips go:

- Make fresh formaldehyde every time from PFA.

- Ideally, you should go from fresh tissue/cells to IP reaction in one go. If you have to freeze your sample at any point, do it at the fixed nuclei stage (fix, quench, lyse the cells and freeze nuclei) or sheared chromatin stage (fix, quench, lyse the cells, lyse the nuclei and shear, freeze sheared chromatin).

- If you do freeze, keep the number of freeze thaw cycles to a minimum.

There is a plethora of ChIP-seq protocols and kits out there. I particularly like ChIP-mentation. But I have to say I've only personally used it with histone marks, not TF ChIP.

Good luck!

Hi, as said there are many protocols in the literature and they mostly depend on you type of cells / organism. Advices given above are useful, you must also be careful with your antibody conjugated beads (especially if they are not magnetic), and perform all the washes very well (do not hesitate to make them quite long). A good fragmentation of you chromatin is also determinant, as well as working on ice constantly and with protease inhibitors. I'm sure that some people in your lab or institute already performed ChIP and can help you, or that you can find a protocol related to your sample type on the web. Good luck!

Hi Aliaksei Z Holik and Fabrice Chatonnet i want to do ChIP sequencing in mouse retina, I wanted to know whether i could dissect the retina and fix it in 1% PFA and then freeze at this point or should i immediately freeze and process the (fix, quench, lyse the cells and freeze nuclei). Which one do you recommend, and should i increase the percentage if it is tissue? instead of 1% to 4%.

I just saw one paper done ChIP seq on mouse retina, the below one Aldiri I, Xu B, Wang L, et al. The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis. Neuron. 2017;94(3):550-568.e10. doi:10.1016/j.neuron.2017.04.022

Is there any suggestions, kindly let me know