Hi all, I'm new here...

I'm doing some practice work on a dataset using Galaxy, and I'm having trouble figuring out where to start. Obviously, I'm just learning - and I'd appreciate some help determining experimental groupings. I'd like to find peaks where FLAG-PKA is recruited over background.

The data files I'm working with are described as follows:

• Total Chromatin from HEK cells (reverse crosslink)
• Total Chromatin from HEK cells (reverse crosslink)
• Anti-Flag ChIP Ctrl HEK wt
• Anti-Flag ChIP Ctrl HEK wt
• Anti-Flag ChIP Ctrl HEK wt
• Anti-Flag ChIP Ctrl HepG2 wt
• Anti-HA ChIP Ctrl HEK wt LPCX
• Anti-HA ChIP Ctrl HEK wt LPCX
• Anti-RNA pol II ChIP HEK wt
• Anti-RNA pol II ChIP HEK wt
• Anti-Flag ChIP HEK PKA-3x-flag
• Anti-Flag ChIP HEK PKA-3x-flag
• Anti-HA ChIP HEK 2-F1 HA-PKA
• Anti-HA ChIP HEK 2-F1 HA-PKA

In the Flag-tagged CHiP data, the endogenous copy of PKA has been tagged with CRISPR. Anti-HA samples are retroviral complemented PKA-HA tagged.

For FLAG-PKA, is the following correct?

• Control - Anti-Flag ChIP Ctrl HEK wt

vs.

• Experimental - Anti-Flag ChIP HEK PKA-3x-flag

And if so, how are Anti-HA and Anti-RNA pol II samples potentially relevant?

If anyone could shed some light on how to arrive at peaks for FLAG-PKA, I'd much appreciate it. Additionally, If anyone would be willing to more generally help me work through this practice exercise, I'd be much indebted.

Thanks so much!