Duration of cross-linking step: 10 minute(s) and 0 second(s)
Specification of the cross-linking agent: Formaldehyde
Other product details
The ChIP was done with the GR antibody (ab3579) for control and dexamethsone treated cells and also an IgG control was included to see if the enrichment is good but we are not able to see a ligand dependent difference.
This was really astonishing to find that the IgG was mich higher than the vehicle control, maybe it needs more optimisation in pre-clearing, or in the washing steps. But we failed with increasing the washes as the amount of IP DNA enriched was getting lower.
We even tried to make two lanes of Solexa sequencing with the DEX-treated samples IP'ed with GR antibody, but all the peaks were too weak to be significantly called as true binding sites after sequencing. When we run our control AR ChIP samples on sequencing in 2 lanes, we get around 15000 binding sites enriched at less than 2% FDR, but with same GR ChIP samples we get around 1000-1500 peaks and the FDR values computed are also too high.
One more thing i would like to point here is this might be completely because of this cell line and the same doesn't hold true for another ones, though we haven't tried ourselves.
Abcam user community
Submitted Feb 02 2010