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Maize Oligonucleotide Array Project |
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Maize Oligonucleotide Array Project FAQ
1. Who may purchase the arrays, and what do I need to do to place an order?
2. How many genes are represented on the array?
3. What is an AZM?
4. What do I need to use the arrays?
5. We have microarray facilities at our institution but we have no experience within our group to do the hybridizations and data analysis.
6. How do I obtain the oligo sequences for all 57,452 oligonucleotides?
1. Who may purchase the arrays, and what do I need to do to place an order?
Long oligonucleotide arrays are currently available to researchers at non profit institutions. The price is $125 for a single 46K slide. A minimum order of 4 slides is required. To place your order, please use our online Order page.
2. How many genes are represented on the array?
46,128 70-mer oligos are printed on a single slide. The selection of oligos for the 46K array was determined by analysis of expression profiles generated for sixteen diverse maize tissues and eliminating oligos from the original two slide set (57,452 oligos in total printed over two slides) that had not reported any significant expression in any of the sixteen tissues. These oligos may represent very weakly expressed genes or not perform well during hybridization due to design issues.
3. What is an AZM?
AZM is an abbreviation for Assembled Zea mays. These are assemblies from the Consortium for Maize Genomics whole genome sequencing project. Details on the AZMs and the different releases can be found here. There are about 9800 AZMs on the array that are not represented in the TIGR Maize Gene Index. Expression profiling experiments using the NimbleGen array system indicates that these sequences are expressed.
4. What do I need to use the arrays?
The arrays are long oligos (70mers) spotted on glass slides. Thus, you will need equipment to perform hybridizations and a scanner for quantifying the hybridization. Protocols describing RNA isolation, labeling and hybridization procedures are available.
5. We have microarray facilities at our institution but we have no experience within our group to do the hybridizations and data analysis.
Maize microarray workshops are held once a year and cover the basics of microarray experimental design, data generation and analysis. Consult the Workshop page for the current workshop schedule.
6. How do I obtain the oligo sequences for all 57,452 oligonucleotides?
The complete set of 70-mer oligonucleotides on the array is now publicly available in bulk downloadable form at http://omad.operon.com/download/index.php. Winzip is required to decompress the files.
Last modified: Thursday, 15-May-2008 09:10:31 MST Last modified: Thursday, 15-May-2008 09:10:31 MST