Whole-genome expression profiling through fragment display and combinatorial gene identification

Nucleic Acids Research
Ats MetsisSten Linnarsson

Abstract

There is a growing demand for highly parallel gene expression analysis with whole genome coverage, high sensitivity and high accuracy. Open systems such as differential display are capable of analyzing most of the expressed genome but are not quantitative and generally require manual identification of differentially expressed genes by sequencing. Closed systems such as microarrays use gene-specific probes and are, therefore, limited to studying specific genes in well-characterized species. Here, we describe Tangerine, a PCR-based system that combines the scope and generality of open systems with a robust and immediate identification algorithm using publicly available sequence information. By combinatorial analysis of three independent and complete DNA indexing profiles, each displaying the complete set of expressed transcripts on capillary electrophoresis, the method allows transcripts to be simultaneously quantified and identified. The method is sensitive, accurate and reproducible, and is amenable to high-throughput automated operation.

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Citations

Jul 8, 2009·Critical Reviews in Food Science and Nutrition·Ulf HammerlingNils-Gunnar Ilbäck
Oct 15, 2008·BMC Genomics·Arne WeibergPetr Karlovsky
May 31, 2007·Algorithms for Molecular Biology : AMB·Koji KadotaMasumi Abe

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