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  • Best protein tag for ChIP

    Anybody have any experience with protein affinity tags for ChIP in human cells. I've tried FLAG-M2 and it gives a lot of background. I also tried the STrEP II-tag and it also gives a lot of background. I'm expressing my protein from a weak promoter so background is more of an issue then using something like a CMV promoter.

    Is there an affinity tag that works really well for ChIP?
    --------------
    Ethan

  • #2
    If background is an issue you can tag with a biotin acceptor site, co-express the biotin ligase BirA and then IP with streptavidin beads which allows you to use a very strong wash.

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    • #3
      I'm using the STrEP II tag/Sterptactin and I either get lots of background or no signal. Streptactin also binds biotinylated proteins. The ChIP works great with antibodies to my protein but I can't get it to work with tagged versions that are not over-expressed. Is the Bio tag better then the STrEP tag for ChIP? Have you tried it with proteins expressed at low levels?
      --------------
      Ethan

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