Kapa vs NEBnext for ChIPSeq?

[JackieM]

Hi Seqanswers!
Forgive me if there’s already a post on this (I saw a post comparing Truseq ChIP kit with NEBnext, but nothing on Kapa) but does anyone have any experience using a Kapa hyper or Kapa Whole Genome Library kit for ChIPSeq? I'll be preparing some ChIP libraries for sequencing on the Hiseq and I was thinking I could just start at end repair with my ChIP DNA, make my own primers and adapters, and adjust their concentrations to the lower input. I’ve had excellent luck with Kapa on whole genome long-insert libraries in the past, but have never started with anything less than a 250ng input of gDNA and would like to use about 5-10ng ChIP DNA for this application.

Does anyone have a general preference between Kapa and NEB when it comes to things like reagent quality, workflow, helpfulness of tech support, etc…? I'm also curious as to how the efficiency of the ligation and amplification reactions in their library kits compare.


Thanks! And I’ll make sure to update this with any info I get.

[nucacidhunter]

Does anyone have a general preference between Kapa and NEB when it comes to things like reagent quality, workflow, helpfulness of tech support, etc…? I'm also curious as to how the efficiency of the ligation and amplification reactions in their library kits compare.

A KAPA poster available in their site: ( http://www.kapabiosystems.com/produc...rep-kits/#docs) claims better performance of their Hyper kit in comparison with NEB Ultra low kit using various amount of sheared E coli DNA input. Their product brochure also has comparison of the kit with both NEB and TruSeq Nano kit. I think they would have credible data for their claim.
I have been happy with NEB Techsupport, but I have not dealt with KAPA one.

[JackieM]

Thanks for the info! That's very helpful!

[JackieM]

Update

We decided to go with KAPA as it's what I'm familiar with, and it has been working beautifully. The kit even survived our freezer going down over a weekend! A previous colleague of mine- you guys may know him as the great Jon Keats- was convinced that they made the greatest ligase/PCR MM on the planet and I found he was generally right about most things NGS. With 10ng input, I'm able to go as low as 4-5 amp cycles (though 4 is really pushing it). I tested the NEBnext Ultra kit, but I over-amplified and we didn't end up sequencing any of the library, so it's hard to compare them directly.

Both seem to be great kits, though. NEB has fantastic tech support (when you can get ahold of them) and they shipped me a kit to test for free. KAPA offered theirs for half price. The downside to using the KAPA kit is that you have to purchase your own, very expensive, adapters. (If you're calculating cost, remember that if you have them HPLC purified and annealed at IDT, you will not get anywhere near the yield that you specified. They may also take a few weeks to arrive.) I believe the KAPA kit is more expensive, so who knows, I may switch to NEB down the road.