Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing
- Equal contributors
Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, Kirkland, Washington 98034, USA
Genome Biology 2003, 4:R66 doi:10.1186/gb-2003-4-10-r66Published: 19 September 2003
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.