We are trying to find FoxP3 interactive domain in WT vs KO mouse regulatory T cells (Treg) through Chip Seq analysis. I am unable to get anything after pulldown although sonitation was good. Antibody is also used in Chip seq and we have been using the same antibody in Co-IP in our lab.
Hello,
Generally the recommended number of cells for ChIP-seq is 10,000,000 cells. I have found that there can be good quality ChIP-seq data from less cells. When you do your ChIP-seq have you tried using a positive control? For example doing a ChIP-seq experiment with POLII such that you can see if you are getting any enrichment. When you say "I am unable to get anything after pulldown although sonication was good." Do you mean that you are not getting any DNA or no enrichment of a known binding site over background? If it is the first remember that with ChIP-seq it is common to only have a few hundred picograms to nanograms of DNA after the chromatin immunoprecipitation. If it is the later I would recommend taking my advice on the positive control and using POL II for the ChIP and then checking a region with which POLII is known to bind via qPCR.
You can also use an alternative approach such as Mint ChIP where you need only a limited cell number.