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We offer microarray technology-based collaboration opportunities to study genome
expression, their regulation, and genome variation. In addition to
Affymetrix's
catalog arrays,
several custom arrays are also available. These custom arrays include
the rice GeneChip® with probes for over 50,000 genes, the wheat GeneChip® with
probes for 38,000 genes, the tomato GeneChip® with probes for 22,000 genes, the
Arabidopsis whole genome GeneChip® with probes covering over 26,000 genes, and
the maize GeneChip® with probes for 80,000 genes. GeneChip® arrays with probes
for plant pathogens Cochliobolus, and Phytophthora are also available.
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A GeneChip® array uses a set of oligonucleotide probes to detect each gene
transcript. One high-density array could contain probes for up to 80,000 genes.
An image of the results of a hybridization is shown to the right.
The GeneChip® array, therefore, can provide researchers with a large quantity of
reproducible data (see scatter plot of two independent hybridizations of RNA
samples, and table below).
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Arabidopsis |
Rice |
| Number of genes per array |
27000 |
51000 |
| Genome coverage |
>95% |
~85% |
| Probe set design |
PM probes only |
PM probes only |
| Number of probes/genes |
14.5 |
10 |
| Feature size |
18 m |
18 m |
| Starting material |
5 g of total RNA |
5 g of total RNA |
| Detection specificity |
1:300,000 |
1:300,000 |
| Dynamic range |
>300 fold |
>300 fold |
| False positives |
<0.2% |
<0.5% |
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Our gene expression analysis is performed using a GeneChip® system from
Affymetrix. The system includes a fluidics station(shown right), a
high-resolution scanner, a controlling computer, and a hybridization oven.
Labeled cRNA samples synthesized from total RNA are used for array
hybridization.
The hybridization signals are detected by the scanner and analyzed by computer
software designed for image processing, visualization, pattern recognition, and
statistical analysis (Figure right).
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