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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.

Author information

  • 1Rosetta 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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