Welcome to the NSF Rice Oligonucleotide Array Project
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Note: Funding for this project ended on September 30, 2007. This site will maintained for the near future. Arrays can still be ordered through the website and are still being printed at the University of California-Davis facility. Please direct all inquires to: Pam Ronald and Janice Pfeiff regarding availability of the arrays. If there are problems with the website, please email ricearray at TIGR.
Xoo Microarray NEW
The oligo design for the new Xanthomonas oryzae array (4658 Xo oligos corresponding to 1000 oligos unique to Xanthomonas oryzae pv oryzae, 1000 oligos unique to Xanthomonas oryzae pv oryzicola and 2500 oligos shared between the 2 genomes) is now complete. These oligos were designed using PICKY. The list of oligos (zip, 138K) and their ORFs (zip, 1.32M) are available for download. The cost is $110 per 5K array. Orders can be placed on the Order Arrays page.
Why Rice Oligonucleotide Arrays?
Microarray technology permits biologists to concurrently measure the expression levels of thousands of genes in a single experiment. Public-access to microarrays is critical to ensure that the public's large investment in rice genomics is converted to public scientific and economic benefits.
Because of its small genome size, extensive genetic map, available genome sequence, and relative ease of transformation, rice is considered a model species for monocots. Gene sequences are relatively conserved among economically agricultural cereal species such as rice, maize, wheat, barley, sorghum, rye, and sugarcane, and therefore, structural and functional analysis of rice has broad practical implications. Draft rice genomic sequence has been generated by Monsanto (japonica cultivar Nipponbare), Syngenta (japonica cultivar Nipponbare) and the Beijing Genomics Institute (indica cultivar). Moreover, >260,000 ESTs and >28,000 full length cDNA sequences are also available.
The International Rice Genome Sequencing Project (IRGSP) has now produced a finished rice (O. sativa spp. japonica cultivar Nipponbare) genome sequence.
The oligo design for the new 45K array (43,312 oligos corresponding to 44,974 TIGR V3 rice gene models) is now complete. The NSF supported rice oligo 45K array was designed using gene models from the TIGR Rice Annotation Database that have EST and/or full-length cDNA support. These oligos were cross referenced to the Kikuchi full-length cDNA dataset and were designed using PICKY. The list of oligos may be downloaded here (zip, 967K). The cost per 45K array will be $110. Orders are now being accepted on the Order Arrays page.
Objectives of the NSF Rice Oligonucleotide Array Project
Rice Oligonucleotide Microarray (ROMA) Expression Database
The ROMA database at TIGR is designed to support expression data from all publicly available rice array platforms including the NSF Rice Oligonucleotide Array Project, Agilent arrays, Affymetrix arrays, and the Yale/BGI oligonucleotide array. Please note that these publicly available data are available at other repositories such as the NCBI Gene Expression Omnibus and in the case of the Yale/BGI array, at the Virtual Center for Cellular Expression Profiling of Rice. Please note that we process the expression data using our methods (see URL) and thus our normalized data may differ from that at other expression databases
Investigators
The NSF Rice Oligonucleotide Array Project is a joint effort by University of California at Davis (UCD), The Institute for Genomic Research (TIGR) and Iowa State University (ISU). The arrays will be printed at ArrayCore at UCD.
Investigators:
The NSF Rice Oligonucleotide Array Project at UCD, TIGR and ISU was funded by the National Science Foundation. The project has since ended but arrays are still being printed at the University of California-Davis facility.
Last modified: Thursday, 01-Nov-2007 17:43:53 EDT