Barcode ChIP-seq library using Bioo Scientific Kit

[inankai]

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?

[Jon_Keats]

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

[advanT]

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.

[ETHANol]

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.

[odile]

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?

[advanT]

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.