Current Status of the NSF Rice Oligonucleotide Array Project
The first print run of the 20k array is complete and available for purchase. The 45k is in preproduction and will be available in November 2005. We invite investigators interested in obtaining our arrays to place an order using our online ordering form
Image from a 20k chip self-self self/self hybridization using rice leaf RNAs.
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Images from a sample hybridization using the 20k array:
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Thumbnail of Hyb 1 print block 1
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Thumbnail of Hyb 2 print block 1
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The samples are from rice leaves treated with wild type Xanthomonas oryzae pv. oryzae culture (Xoo) vs. a mutant Xoo control. 2ug of mRNA was used for indirect labeling. The probe was hybridized at 55C in Geneframes buffer from MWG. Slides were scanned using an axon 4000 scanner and spot finding was done using Genepix. 063714 and 063715 are dye swaps of the same RNA sample.
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Our second version of the array "Rice oligo version 2" contains 20,230 oligonucleotides which were 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. They are now being printed at UCD and slides can now be ordered through this web site (order form). The cost is $110/slide.
If requested, ArrayCore is able to provide a hybridization service. Users should send their labelled probes vacuum centrifuged and ready to hybridize (ArrayCore will supply protocols for recommended procedures). The current rate for off-campus users who would like to use the hybridization service is $678.26 for 4-12 slides (4 slides minimum). This includes the cost of the hybridization, scanning, and spot-finding analysis. This works out to be $56.52 per slide (assuming 12 slides). The raw data will then be sent to the user for analysis. Iobion GeneTraffic Duo is available for data analysis by ArrayCore users via our webserver and the cost associated with this service for off-campus users is $24.16 per slide.
TIGR is also in the process of developing a Rice Oligonucleotide Microarray Database which will allow users to store expression data generated from the arrays as a free service. Expression data submitted will be analyzed and available for comparative studies with all publicly available rice array data. The expression database aims for complete compliance with the MIAME and Plant Ontology standards that have been developed.
Last modified: Friday, 14-Oct-2005 10:14:07 EDT