International Mammalian Genome Society

logo18th International Mouse Genome Conference

17-22 October 2004, Seattle, USA


POSTER 83 - DEVELOPMENT OF A WHOLE MOUSE GENOME MICROARRAY WITH EMPIRICALLY OPTIMIZED 60-MER OLIGONUCLEOTIDE PROBES USING AGILENT’S SUREPRINT TECHNOLOGY

Collins PJ, Sun H, Gao J, Nguyen K, Lin E, Doan TB, Giles S, Tang S, Fulmer-Smentek SB, Shannon KW, Webb PG

Agilent Technologies, Inc., Palo Alto, United States

The explosion in mouse genomic sequence availability in recent years has enabled the development of whole genome microarrays with the potential to revolutionize fundamental research.  Agilent’s whole mouse genome microarray was developed using a powerful validation process in which optimal probes were empirically selected to represent each gene in the mouse genome.  The first step was to define the set of gene elements by grouping transcript sequences from well-established public sources, such as RefSeq, Riken, NIA, and Ensembl, based on their similarities to one another and their overlap on the mouse genome.  Next, consensus sequences covering all the high quality transcripts in each of these gene bins were defined, and a set of ten candidate 60-mer probe sequences were computationally determined to represent each consensus region.  These candidate probes were hybridized with ten differentially expressing sample pairs.  From the resulting data one optimal probe was selected from each candidate set to specifically represent each consensus region.  Probes were selected to represent additional transcripts to ensure whole genome coverage.  The final set of 60-mer oligo probes have been in situ synthesized to create a 44,000-feature microarray format using Agilent’s SurePrint technology.  In this presentation we describe the novel probe selection process used in developing this whole genome microarray.  In addition, we demonstrate some aspects of the performance of this microarray in measuring differential gene expression.

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