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Old 10-15-2012, 04:00 AM   #2
TonyBrooks
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Location: London

Join Date: Jun 2009
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What application are you specifically looking at? RNA-Seq, DNA-Seq, ChIP-Seq, other...
What level are you looking to plex (12, 48, 96, higher?)
IMHO indexing primers are the most over-priced aspect of NGS. If you think you are going to be doing a lot of index library preparation, you may want to look at making your own.

http://www.ncbi.nlm.nih.gov/pubmed/21431778

We ordered a set of indexes based on the above paper and use them regularly for both indexed (and non-indexed runs - you don't need to read the barcode). It works to be significantly cheaper per reaction than buying commercially, but there is obviously a largish initial outlay on the HPLC oligos. (Of course, you don't need to order all 96 in one go - one synthesis should provide enough for hundreds of reactions).
Those oligo sequences work well on the GAIIx, HiSeq and MiSeq - just remember to use the custom index sequencing primer.

There are also people on here dabbling with homebrew dual indexing, which is something we may look at in the future. It cuts the number of oligos you need to order down and will hopefully be scalable to >96 plex.

Last edited by TonyBrooks; 10-15-2012 at 04:03 AM.
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