Question: Histone modification peaks to compare with my ChIP-seq peaks
1
gravatar for fhassanz
3.6 years ago by
fhassanz10
fhassanz10 wrote:

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,

ADD COMMENTlink modified 3.6 years ago by jotan1.2k • written 3.6 years ago by fhassanz10
3
gravatar for jotan
3.6 years ago by
jotan1.2k
Australia
jotan1.2k wrote:

"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.

ADD COMMENTlink written 3.6 years ago by jotan1.2k

Great! Thank you very much.

ADD REPLYlink written 3.6 years ago by fhassanz10
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