experimental design of ChIP-Seq

[aquleaf]

Hi all. I have a question regarding the experimental design of ChIP-Seq. We have cells in two different states, and we would like to compare the binding profile differences between two states. Should we keep the cell amounts used in the ChIP the same?

By the way, could anyone recommend a tool to analyze the binding profile differences?

Thanks very much! Any suggestion will be greatly appreciated.

[dariober]

We have cells in two different states, and we would like to compare the binding profile differences between two states. Should we keep the cell amounts used in the ChIP the same?

In general I would say yes, if possible. Since you want to detect differences between states you should keep everything the same between cells except for the "state" variable I.e. randomize possible confounding factors between the two state groups so that the differences can be attributed to the state condition.

By the way, could anyone recommend a tool to analyze the binding profile differences?

Have a look at these tools (there should be more): MMDiff: quantitative testing for shape changes in ChIP-Seq data sets and DiffBind