Technical Note, Array Design and Performance of the GeneChip® Mouse Expression Set 430

Since the success of an array design is highly dependent on the quality and curation of sequence information, we built tools to address these issues during the design of the GeneChip Human Genome U133 Set (HG-U133).* We then leveraged the knowledge gained from this process and applied a similar method to the GeneChip Mouse Expression Set 430 (Mouse 430) design. The design modifications for the Mouse 430 are detailed below. Various public data sources were used for the Mouse 430 design (Table 1). Sequence data were obtained from dbEST (NCBI, June 2002), GenBank (NCBI, Release 129, April 2002), and RefSeq (NCBI, June 2002). Additionally, the draft assembly of the mouse genome (Whitehead Institute Center for Genome Research, April 2002) was used to assess sequence orientation and quality. The initial sequence curation process involved: