Nature Biotechnology
20, 353 - 358 (2002)
doi:10.1038/nbt0402-353
Profiling alternative splicing on fiber-optic arraysJoanne M. Yeakley1, 2, Jian-Bing Fan3, Dennis Doucet3, Lin Luo3, 4, Eliza Wickham3, Zhen Ye1, Mark S. Chee3
& Xiang-Dong Fu11
Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093. 2
Current address: Illumina, Inc., 9885 Towne Centre Drive, San Diego, CA 92121. 3
Illumina, Inc., 9885 Towne Centre Drive, San Diego, CA 92121. 4
Current address: Johnson & Johnson Pharmaceutical Research & Development, L.L.C., 3210 Merryfield Row, San Diego, CA 92121.
Correspondence should be addressed to Xiang-Dong Fu xdfu@ucsd.edu or Jian-Bing Fan jfan@illumina.comThe human transcriptome is marked by extensive alternative mRNA splicing and the expression of many closely related genes, which may be difficult to distinguish using standard microarray techniques. Here we describe a sensitive and specific assay for parallel analysis of mRNA isoforms on a fiber-optic microarray platform. The method permits analysis of mRNA transcripts without prior RNA purification or cDNA synthesis. Using an endogenously expressed viral transcript as a model, we demonstrated that the assay readily detects mRNA isoforms from as little as 10−100 pg of total cellular RNA or directly from a few cells. Multiplexed analysis of human cancer cell lines revealed differences in mRNA splicing and suggested a potential autocrine mechanism in the development of choriocarcinomas. Our approach may be useful in the large-scale analysis of the role of alternative splicing in development and disease.
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