International Mammalian Genome Society

The 16th International Mouse Genome Conference (2002)


POSTER 38 - DESIGN AND VALIDATION OF A NOVEL 22,000 FEATURE IN SITU-SYNTHESIZED 60-MER OLIGONUCLEOTIDE MICROARRAY FOR STUDIES OF EARLY DEVELOPMENT AND STEM CELLS

M Carter
Developmental Genomics & Aging Section, Laboratory of Genetics; National Institute on Aging, NIH

1) Hamatani T,  1) Sharov A,  2) Carmack C,  1) Qian Y,  2) Brzoska P,  2) Hwang S,  1) Ko M
1) NIA,  2)Agilent

Inkjet-based in situ 60-mer oligo synthesis technology allows more rapid and flexible microarray design without labor-intensive clone handling required by cDNA array production. However, for downstream experimental work on genes implicated by microarray experiments, a collection of readily available cDNA clones corresponding to these oligos is essential. 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.As an initial performance assessment, we have generated oligo array expression profiles of mouse E12.5 embryo and placenta and compared them to similar profiles previously published using the NIA 15K cDNA microarray platform. For over 11,000 unique genes represented on both platforms, we compared the expression ratios obtained and their statistical significance.  The oligo array measured more significant expression changes than the cDNA array, especially at low expression ratios, and many genes which gave little or no signal on the cDNA array produced reliable measurements in the oligo system.  A number of genes were measured by real-time PCR for comparison, and differences between the data sets are being examined in detail.  Labeling protocols for very small samples were developed to allow expression profiling of rare early developmental tissues and purified stem cells, and the performance of these protocols was tested on arrays.


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