PCR Primer 1.1 or PCR Primer PE 1.0

[kameha]

Hey,
I plan to do a ChIP-Seq on the Illumina GA II. According to Illumina´s ChIP-Seq protocol, they use the primer pair PCR primer 1.1 and PCR primer 2.1 to amplifiy the library (ie adding the adapters).
But reading about the paired end read method, another primer pair was mentionend: the PCR primer PE 1.0 and 2.0
Does this mean, ChIP-Seq is not sequenced by paired end read, but only by single end read?
Or do I have to use the PCR primer PE 1.0 and 2.0 to do paired end read?
Looking forward to your answers!

[kcchan]

PCR 1.1 and 2.1 are shorter versions of the older 1.0 and 2.0 primer pairs. The adapters themselves are actually ligated in the step before PCR. You should have no problems doing a paired end read using primer pairs 1.1 and 2.1. However, I don't have exact experience with ChIP-seq so you should ask Illumina technical support to confirm.

[jomitsui]

PCR Primer 1.1 and 2.1 are indeed Single read primers, it only contains the binding site of Read 01 sequencing primer. If you need paired end run for your ChIP-Seq, I suggest that you use the PCR PE 1.0 and 2.0 primers.

Illumina have just launched a new TruSeq ChIP-Seq kit for PE run, and I heard NEB selling the PE version of the ChIP-Seq kit too.