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Nat Methods. 2009 Sep;6(9):647-9. doi: 10.1038/nmeth.1360. Epub 2009 Aug 9.

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis.

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  • 1Department of Molecular Informatics, Rosetta Inpharmatics LLC, a wholly owned subsidiary of Merck and Co., Inc., Seattle, Washington, USA. christopher_armour@merck.com


We developed a procedure for the preparation of whole transcriptome cDNA libraries depleted of ribosomal RNA from only 1 microg of total RNA. The method relies on a collection of short, computationally selected oligonucleotides, called 'not-so-random' (NSR) primers, to obtain full-length, strand-specific representation of nonribosomal RNA transcripts. In this study we validated the technique by profiling human whole brain and universal human reference RNA using ultra-high-throughput sequencing.

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