Histone modification peaks to compare with my ChIP-seq peaks

Question

[fhassanz]

I have a very basic question. I have done a ChIP-seq on TT2 mouse ES cells using my antibody. Where can I find the Bed file containing ChIP-seq peaks for different Histone modifications? Do I have to compare with histone modification ChIP peaks obtained from the same mouse ES cells (TT2) or using any mouse ES cells are acceptable?

Thanks,

Answer 1

[jotan]

"Do I have to compare with histone modification ChIP peaks obtained from the same mouse ES cells (TT2) or using any mouse ES cells are acceptable?"

The answer is: it's context dependent. If you wanted to do very fine, detailed work (e.g. does a particular SNP influence the binding of my transcription factor?) then the cells would have to be as closely matched as possible (clonal). If you're looking for broad, general patterns (e.g. does my transcription factor follow active or silencing modifications?), then an equivalent cell type would be acceptable although obviously, a closer match is more desirable.

As with all NGS sequencing Encode and GEO are the best places to start. Search for ES cells and histone mods.

[fhassanz]

Great! Thank you very much.