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I found the link to a commercial product by Evrogen to normalise cDNA samples for gene discovery projects here:
http://www.evrogen.com/technologies/normalization.shtml

The most up-to-date reference seems to be this Curr Protoc Mol Biol. paper by Bogdanova et al.: http://www.ncbi.nlm.nih.gov/pubmed/20373503

They claim their method is compatible with nextgen sequencing platforms:

cDNA normalization using duplex-specific nuclease (DSN) is a highly efficient approach that can be applied for normalization of full-length-enriched cDNA (Zhulidov et al., 2004; Zhulidov et al., 2005). The resulting cDNA contains equalized abundance of different transcripts and can be used for construction of cDNA libraries and for direct sequencing, including high-throughput sequencing on the next generation sequencing platforms (Roche/454, ABI/SOLiD or Illumina/Solexa).

Has anybody successfully used it for next-gen gene discovery projects?

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closed as not constructive by jonsca, Luke, Rory M Aug 27 '12 at 21:37

As it currently stands, this question is not a good fit for our Q&A format. We expect answers to be supported by facts, references, or expertise, but this question will likely solicit debate, arguments, polling, or extended discussion. If you feel that this question can be improved and possibly reopened, visit the help center for guidance.If this question can be reworded to fit the rules in the help center, please edit the question.

    
This seems to be more like a poll than a question. –  jonsca May 1 '12 at 11:48
    
Can I turn it into a poll in this website? –  149781-32509185 May 2 '12 at 7:26
    
No, I meant more that poll-type questions can be closed as "not constructive". You should probably reword it a bit to prevent this. –  jonsca May 2 '12 at 10:02

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