Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing.
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ABSTRACT:
SUBMITTER: Castle J
PROVIDER: S-EPMC328455 | biostudies-literature | 2003
REPOSITORIES: biostudies-literature
Publications
Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing.
Castle John J Garrett-Engele Phil P Armour Christopher D CD Duenwald Sven J SJ Loerch Patrick M PM Meyer Michael R MR Schadt Eric E EE Stoughton Roland R Parrish Mark L ML Shoemaker Daniel D DD Johnson Jason M JM
Genome biology 20030919 10
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 iso ...[more]
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