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Old 11-16-2011, 11:41 AM   #1
inankai
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Default 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?
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Old 11-16-2011, 11:49 AM   #2
Jon_Keats
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I don't use the kit but how do you quantify the input DNA? Also, how do you do the post adaptor size selection?
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Old 11-17-2011, 06:54 AM   #3
advanT
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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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Old 11-17-2011, 07:04 AM   #4
ETHANol
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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.
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Old 11-17-2011, 11:01 AM   #5
odile
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Quote:
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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Old 11-17-2011, 08:11 PM   #6
advanT
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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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