Indexed Mate Pair Library Prep for GAIIx/High Seq

[busypops]

Does anyone have any experience of preparing indexed mate pair libraries for sequencing in the GAIIx or HiSeq 2000?
I have successfully produced 3kb insert size mate pair libraries but this time I need to produe a 3 and 6kb, index them and pool them for one lane.
Anyone else trued this?

Thanks in advance

[JakobHedegaard]

Why not simply use the "Index PE Adapter Oligo Mix" from the Illumia 12-plex kit instead of the normal "PE Adapter Oligo Mix" supplied with the mate-pair kit? Then you can build in the indexes (index #6 and #12 for 2-plex) during the PCR.
I have produced mate-pair libraries with insert sizes up to 10 Kb - but not indexed. But I would like to know if it works :-)
Cheers, Jakob

[busypops]

Thanks for your reply I was planning on using the IN PE Adapter Oligo mix then using 2 indexes at PCR stage as you said. I will post and let you know how it goes.
I'm glad to hear that you were able to produce mate pair libraries with larger insert size, hope it works for me too

Cheers

[barrmur]

As a add on,

Is it possilbe to multiplex 8 mate pair libraries with 8 Nextera libraries on a HiSeq? If so what would be the best wat to go about it?