Hello everyone, I am performing ChIP seq in tumor cell lines to find target genes of a specific transcription factor. There is no antibody for my protein, so I am using anti-HA antibody.

For each cell line, I have anti-HA expressing cells and empty vector. Besides, for each one of these, I have a ChIP control (INPUT/No antibody) and a IP-sample (with the antibody). This way:

Sample1= Cell line 1/empty vector - Input

Sample2= Cell line 1/empty vector - Anti-HA

Sample3= Cell line 1/expressing vector - Input

Sample4= Cell line 1/expressing vector - anti-HA

For regular ChIP-seq (using a specific antibody) performed previously in my lab, I have sequenced Input and IP samples, using the input to removing noise in the bioinformatics analysis.

My question is, do I have to sequence the empty vector samples (1 and 2) as well?

And if so, how this data is going to be useful for peak calling in my bioinformatics analysis?

I hope I have been clear in my question,

*P.s. I also made anti-IgG and H3 controls.

Thanks a lot for any help!