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    Genome Biol. 2003;4(10):R66. Epub 2003 Sep 19.

    Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing.

    Castle J, Garrett-Engele P, Armour CD, Duenwald SJ, Loerch PM, Meyer MR, Schadt EE, Stoughton R, Parrish ML, Shoemaker DD, Johnson JM.

    Source

    Rosetta Inpharmatics, Merck & Co, Inc, 12040 115th Ave NE, Kirkland, Washington 98034, USA.

    Abstract

    Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. These optimized protocols can be used to detect small variations and isoform mixtures, map the tissue specificity of known human alternative isoforms, and provide a robust, scalable platform for high-throughput discovery of alternative splicing.

    PMID:
    14519201
    [PubMed - indexed for MEDLINE]
    PMCID: PMC328455
    Free PMC Article

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