Explanation About Illumina Dpnii Gex Adapter And Illumina Nlaiii Gex Adapter?

Question

[deepthithomaskannan]

Hi all,

What is Illumina DpnII Gex Adapter and Illumina NlaIII Gex Adapter? Anybody can help me to understand what are these adaptors?

Thanks, Deeps

Answer 1

[Steve Lianoglou]

Illumina had kits to perform high throughput SAGE sequencing. Here is a PDF of one of the protocols. The library prep was something like what was used in this study by Wu et al.

There are many resources to look through to find how old school SAGE libraries are built. You can check out this one. Follow those steps just before they perform "concatemerization" and pretend the light blue sequences on either side of the "insert" are adapters that make this library (the rainbow colored bits) amenable to sequencing on a GAII or HiSeq.

Now, a critical step in building a SAGE library is using an anchoring enzyme (DpnII or NlaIII) which essentially defines the 5' end of the tag you will sequence per transcript. The different adapters you mention are used for these different enzymes.

This answer will make more sense to you as you learn how this library prep is done, so take some time to figure that out if you want to ask a follow up question.