title: Multiplex cDNA quantification method that facilitates the standardization of gene expression data.
abstract: Microarray-based gene expression measurement is one of the major methods for transcriptome analysis. However, current microarray data are substantially affected by microarray platforms and RNA references because of the microarray method can provide merely the relative amounts of gene expression levels. Therefore, valid comparisons of the microarray data require standardized platforms, internal and/or external controls and complicated normalizations. These requirements impose limitations on the extensive comparison of gene expression data. Here, we report an effective approach to removing the unfavorable limitations by measuring the absolute amounts of gene expression levels on common DNA microarrays. We have developed a multiplex cDNA quantification method called GEP-DEAN (Gene expression profiling by DCN-encoding-based analysis). The method was validated by using chemically synthesized DNA strands of known quantities and cDNA samples prepared from mouse liver, demonstrating that the absolute amounts of cDNA strands were successfully measured with a sensitivity of 18 zmol in a highly multiplexed manner in 7 h.
authors.affiliation: Department of Life Sciences and Institute of Physics, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
authors.forename: Osamu
authors.initials: O
authors.lastname: Gotoh
authors.forename: Yasufumi
authors.initials: Y
authors.lastname: Murakami
authors.forename: Akira
authors.initials: A
authors.lastname: Suyama
mesh_terms: D000818:Animals; D002232:Carbocyanines; D018076:DNA, Complementary / Q000032:analysis*; D005456:Fluorescent Dyes; D020869:Gene Expression Profiling / Q000379:methods / Q000592:standards*; D008297:Male; D051379:Mice; D008807:Mice, Inbred BALB C; D020411:Oligonucleotide Array Sequence Analysis
chemical_list: D002232:Carbocyanines; D018076:DNA, Complementary; D005456:Fluorescent Dyes; C089187:cyanine dye 3; C085321:cyanine dye 5