I'm currently performing ChIP-qPCR using the ChIP-IT® Express Kit (Active Motif) in parental HepG2 cells to study THRB binding. However, I suspect that the antibodies I’ve used may not be working well—I’ve already tried THRB antibodies from two different suppliers, but the results have been inconsistent.

For transcription factors like THRB, would it be more effective to use a THRB-overexpressing cell line instead of parental HepG2 cells? Also, could anyone recommend a well-validated, ChIP-grade THRB antibody that has worked reliably in your hands?

Any suggestions regarding kits, antibodies, or optimization strategies would be greatly appreciated.

Another point is:

I have generated stable HepG2 cells expressing Lenti6-Flag-sTurboID-high-N-TRβ1. I’m considering using chromatin affinity purification instead of antibody-based ChIP to pull down TRβ1-bound DNA.

Has anyone successfully used Flag-tag-based pulldown to enrich for DNA regions bound by transcription factors? Would this approach give better signal compared to ChIP, especially if antibodies against TRβ1 are unreliable?

Also, I’d appreciate any advice on optimizing this approach or examples of similar experiments using tagged transcription factors.