4.5 years ago by
"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.