TRANSCRIPTOME 2002: From Functional Genomics to Systems Biology
March 10-13, 2002
Seattle, Washington, USA

A Novel 22,000 Feature In Situ-Synthesized 60-Mer Oligonucleotide Microarray: Expression Profiling Of E12.5 Mouse Embryo and Placenta

Mark G. Carter1, Condie E. Carmack2, Yong Qian1, Toshio Hamatani1, Pius Brzoska2, S. Stuart Hwang2, and Minoru S.H. Ko1, 1Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging (NIA), National Institutes of Health (NIH), Baltimore, MD 2Agilent Technologies, Palo Alto, CA

Inkjet-based in situ 60-mer oligo synthesis technology has opened the door for more rapid and flexible microarray design without the labor-intensive clone handling required by cDNA array production. However, for downstream experimental work on genes implicated by microarray experiments, it is essential to have the collection of readily available cDNA clones corresponding to these oligos. To this end, we have designed and constructed an in situ-synthesized microarray representing approximately 21,000 unique genes, at least 98% of which correspond to clones in the unique cDNA collections of NIA (see the abstract by Ko et al. in this meeting). As an initial performance assessment of this microarray, we have generated expression profiles of mouse E12.5 embryo and placenta and compared them to similar profiles previously published using the NIA 15K microarray platform. For over 11,000 unique genes represented on both platforms, the oligo platform measured over six times more statistically significant expression changes than the cDNA array, with more stringent statistical criteria.  Twenty percent of genes which gave little or no signal in one or more channels using the cDNA array produced reliable measurements in the oligo system. Similarities and differences between the two data sets are being examined in detail.

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