ChIP-seq: input sequencing

[gege_55]

Hi all,

I am planning to do a ChIP-seq experiment on whole insect embryos. I have 3 histon modification antibodies and one transcription factor antibody. Furthermore I have two independent chromatin preparations as the biological duplicates. Now I want to do the ChIP's with my four antibodies on both chromatin preps.
My question is if I need to do the input sequencing for each ChIP or if it is OK to just do one input sequencing for the two chromatin preps and use it for all the ChIP's. Instead of 16 sequencing runs (2x4 ChIP and 2x4 input) I would have to do only 10 (2x4 ChIP an 2x1 input).

Best wishes,
Georg

[kopi-o]

In theory, it should be sufficient to sequence each input once in this case. You want to have about the same sequence coverage for ChIP and input in each case though (peak calling does not work well if the input library is smaller than the ChIP library) so you may want to sequence the inputs a bit more to be safe (e g 2x2).