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

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.

SUBMITTER: Castle J 

PROVIDER: S-EPMC328455 | biostudies-literature | 2003

REPOSITORIES: biostudies-literature