Illumina workflow, methods and equipment

[apfejes]

I generally only deal with the post-lab stuff (eg. aligning, analysis, etc), though if you have specific questions, I can ask the lab people here who would know the answers.

[ECO]

Great thread. I'd like to get a hold of the Illumina RNA tagging library prep protocols as a resource, as I've been asked multiple times.

[ScottC]

Hi Everyone,

We're just getting our sequencer installed and running at the moment, so I'd be interested in talking with people who are either in the same position, or who already have theirs up and running. I'd be interested in starting some discussion on the methods that people are using for their sample prep, differences from the 'standard' illumina protocols, workflows and so forth. Is anyone else interested in sharing their experiences?

For example, what shearing method(s) are you using? Standard Illumina nebulisers, sonication, focussed acoustic shearing etc? I've heard a few people are ditching the nebuilsers because they can't get the fragmentation down to a small enough size, or that the yield is too low. What about cleanup of the DNA? Is anyone using SPRI, HPLC, or standard gels?

Cheers,

Scott.