Question: ChIP-seq: Should we be consistent with the control used (IgG/Input) among different conditions?
0
gravatar for salamandra
3 months ago by
salamandra130
salamandra130 wrote:

Imagine this situation with ChIP-seq analysis.

We have to conditions: A and B. For each condition there are three samples: one is ChIP, the other two are the controls (IgG and Input). For sample A the control with best quality (with higher number of reads and that passes QC) is IgG and for sample B the control with best quality is Input. If we want to compare condition A with condition B, should we use the same control in both conditions regardless of the quality of that control or can we use different controls for different conditions (IgG for A and Input for B)?

chip-seq controls • 242 views
ADD COMMENTlink modified 3 months ago by Devon Ryan80k • written 3 months ago by salamandra130
2
gravatar for Devon Ryan
3 months ago by
Devon Ryan80k
Freiburg, Germany
Devon Ryan80k wrote:

You should always use the same type of control, which should always be input. In my opinion IgG is a waste of sequence, it's replaceable with a blacklist.

ADD COMMENTlink written 3 months ago by Devon Ryan80k

What about H3 ChIP-seq as control? As H3 gives nucleosome occupancy, do you think it might be more appropriate instead of Inputs?

ADD REPLYlink written 3 months ago by sikhtechai30

For some specific questions, sure. With that you're asking less "where's the enrichment of my modification" and more "where's the enrichment of my modification above where one would normally expect it assuming it's evenly distributed among H3 instances". For most cases a standard input would make more sense, but on occasion the aforementioned question is relevant.

ADD REPLYlink written 3 months ago by Devon Ryan80k

Makes sense! Thank you very much!

ADD REPLYlink written 3 months ago by sikhtechai30
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