Multiplex adapters and indexes for Illumina HiSeq

[upenn_ngs]

We have found that the amplification with a three primer system (multiplex pcr 1.0, multiplex pcr 2.0, and pcr primer index #) does not yield good results. This is the original illumina design. However, multiplex pcr 2.0 and the pcr primer index # oligos have homology and can be ordered as a single, longer primer. This two primer system will yield quality indexed libraries.

[arg]

Hi upenn_ngs,
thanks a lot for your answer. We did not get the TruSeq kit because ordering pretty much everything from IDT was 1/3 of the price...If they decrease the price that much we would start thinking about it....or if the custom made stuff don't work.
And thanks for the tip about pcr primers and indexes, but what exactly you mean with pcr 2.0 designed as a single primer?
Thanks!

[upenn_ngs]

The truseq kits from illumina are more reasonably priced than the previous generation (~$50/sample for enzymes and oligos).

We have had success ordering from IDT with HPLC purification. For multiplex, I recommend using a two primer system (illumina index and PCR 2.0 sequence designed as a single primer).

[arg]

Dear all,
we are planning on multiplexing our samples in the new HiSeq Illumina we have available. The kits are so extremely expensive that they are not even an option . But many people told us that we can get our own primers/adapters/indexes custom made from IDT. We got custom made adapters for paired end sequencing with the GA and they had a phosphorothioate bond.
Has anybody got these things custom made and know how are all of them purified?
Thanks!!