Information of the Microarray can be found at www.ggbio.com/rice60kchip.html (GreenGene Biotech). The 60 K Microarray was designed to represent all the genes in rice. In total, 60,727 oligomers were designed from gene-specific regions of both japonica and indica subsp. These include 58,417 from known and predicted genes and 66 randomized DNA. Among these, 2,310 genes were also designed as antisense oligomers. Oligomer sequences were extracted by Qiagen-Operon (Cologne, Germany) based on rice genome information from Beijing Genomics Institute (Yu et al., 2002). Oligomers were synthesized and purified by Qiagen-Operon and spotted on SuperAmine slide using facilities of the Dr. David Galbraith lab at the University of Arizona (http://ag.arizona.edu/microarray/deconvolution.html). A set of Rice 60 K Microarray is composed of 2 slides and has a total of 64,896 spot addresses. Each slide is formatted with 48 (12 x 4) blocks with addresses composed of 676 (26 x 26) spots. Blank spots (4,099) were also included for easy alignment of scanning format. Each oligomer, 70 nucleotides long and average melting temperature of 78°C, was printed in each spot address with a diameter of 100 µm.
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Description
Oryza sativa Genome Oligo Set Version 1.0 was designed by Beijing Genomics Institute (BGI) and contain 60,727 70mer oligos representing both indica and japonica genomes. All oligos were designed from cDNAs, expreseed sequence tag (EST) sequences, predicted genes of BGI rice genome build and other public resources. Mapping to TIGR rice genome pseudommolecues release 2 is based on the BLAST results, if an oligo has greater than 97% identity to a gene sequence from TIGR pseudomolecules, the oligo represents that gene. If the oligo matches to multiple genes, only one gene ID is randomly chosen. Preference is given to a 100% match.
