title: Whole-genome expression profiling through fragment display and combinatorial gene identification.
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.
authors.affiliation: Global Genomics AB, Tomtebodavägen 21B, SE-171 77 Stockholm, Sweden.
authors.forename: Ats
authors.initials: A
authors.lastname: Metsis
authors.forename: Ulf
authors.initials: U
authors.lastname: Andersson
authors.forename: Göran
authors.initials: G
authors.lastname: Baurén
authors.forename: Patrik
authors.initials: P
authors.lastname: Ernfors
authors.forename: Peter
authors.initials: P
authors.lastname: Lönnerberg
authors.forename: Andreas
authors.initials: A
authors.lastname: Montelius
authors.forename: Mats
authors.initials: M
authors.lastname: Oldin
authors.forename: Arno
authors.initials: A
authors.lastname: Pihlak
authors.forename: Sten
authors.initials: S
authors.lastname: Linnarsson
mesh_terms: D000818:Animals; D002460:Cell Line; D020869:Gene Expression Profiling / Q000379:methods*; D016678:Genome; D023281:Genomics / Q000379:methods*; D051379:Mice; D016133:Polymerase Chain Reaction / Q000379:methods*; D012333:RNA, Messenger / Q000032:analysis / Q000378:metabolism; D015203:Reproducibility of Results
chemical_list: D012333:RNA, Messenger