Bias between NEBnext and Truseq RNA kits?

[iquigley]

Hey gang, I've got a bunch of samples already sequenced with libraries built with Illumina's truseq v2 kits. I have a few left to do but am running into the small-potatoes user problem of not needing 48 reactions and am thus loathe to buy another full v2 kit. I also have a strong suspicion that NEB provides the enzymes for those kits. So: has anybody here ever tried to compare libraries made by truseq with libraries of the same RNA made with NEBnext? If there's very little bias, I will be sorely tempted to go that route.

Thanks for any insights!

[rnaeye]

There is some data showing polymerase bias:

https://www.neb.com/products/m0541-nebnext-high-fidelity-2x-pcr-master-mix

[SeqMonster]

NEBNext RNA library prep kit - For Single-end or Paired-end?

Does anyone know whether the multiplex oligos for NEBNext RNA library prep kit allow for paired-end sequencing, and compatible to MiSeq? There is only one index primer added onto the PCR reaction, together with the universal primer.

[DRod]

Yes. The NEBNext multiplex oligos are compatible with paired-end sequencing and MiSeq.
Here a link to a series of webinars you might find useful:
http://neb-online.de/index.php/de/neb-aktionen/260

[windhorse8]

Yes. The NEBNext multiplex oligos are compatible with paired-end sequencing and MiSeq.
Here a link to a series of webinars you might find useful:
http://neb-online.de/index.php/de/neb-aktionen/260

How about NEBnext multiplex small RNA library prep set (cat. no. E7330S) ? Is library prepared using this kit also compatible with Miseq ? Do I have to send separate custom primer since custom primer read seems to be different from what is found on Truseq universal adapter sequence.
Thanks

[rnaeye]

Yes, it's compatible with Miseq. You do not need separate primers. You can give them a call to double check if you like.