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  • chip seq

    Hi everyone,

    We will be in the lab using chip seq technology for the first time and i was wondering what is best to use as control, input dna or mock. I guess input is better but i want to hear what people do usually. We will be mainly checking for three different histone marks; I was wondering what will be the kind of antibody to use : monoclonal or polyclonal knowing that monoclonal might result in few dna bound that will be difficult to discriminate above the control in the chipseq output and the polyclonal could yield in unspecific bound dna. I know that I will have to go for tests at a small scale with specific sequences, do pcr after chip and see how it looks with the appriopriate controls but again just want to hear what you guys are usually doing. The marks we will be testing are H3K4me2, H3K9me2 and H3K27 me3.
    Thanks in advance for your advice.

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