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  • Barcode ChIP-seq library using Bioo Scientific Kit

    Anyone has experience with the Bioo Scientific Kit for multiplexing ChIP-seq library.

    I just get their ChIP-seq kit barcode-6, but I found there is heavy primer dimer contamination in the final PCR product.

    What can I do to remove the dimers?

  • #2
    I don't use the kit but how do you quantify the input DNA? Also, how do you do the post adaptor size selection?

    Comment


    • #3
      I would do a double Ampure bead cleanup after PCR.

      Are you just using their barcode kit? We are using both their Chip-Seq library prep kit and barcode kit and are very happy with our sequencing results so far. They are using a nifty technique in their sample prep that seems to work well with low nanogram / picrogram inputs. I haven't seen primer dimer in our preps, we do double ampure pure cleanup after PCR.

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      • #4
        Just run it on an agarose gel and cut out the sample leaving the adapter dimers behind and purify on Qiagen minElute. Ampure could work as well.
        --------------
        Ethan

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        • #5
          Originally posted by advanT View Post
          I would do a double Ampure bead cleanup after PCR.

          Are you just using their barcode kit? We are using both their Chip-Seq library prep kit and barcode kit and are very happy with our sequencing results so far. They are using a nifty technique in their sample prep that seems to work well with low nanogram / picrogram inputs. I haven't seen primer dimer in our preps, we do double ampure pure cleanup after PCR.

          Advant, what do you mean by "we do double clean-up"? You clean up twice with the same ratio beads/DNA? Why isn't one clean-up enough?

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          • #6
            odile,

            yes, double cleanup with 1X beads. I haven't ever tried it with one cleanup, I'm guessing double cleanup might be more effective. It also avoids the need to run an agarose gel.

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