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Project Documentation & Protocols: Maize Gene Discovery Project: Microarrays: Overview

Contents: Index | Progress | Controls | Libraries | Arrays | Data | Protocols | Ordering | Links | FAQs

Microarrays are produced in the laboratory of Dr. David Galbraith at the University of Arizona, by Dr. Rangasamy Elumalai, Hakan Ozkan, and Maya Gchachu.

The EST collection consists of a series cDNA libraries prepared from different maize tissues (see EST project information). Purified plasmid DNA (remaining after individual EST items were sequenced at Stanford University) was delivered to the University of Arizona for PCR amplification of the cDNA insert. Gel electrophoresis was used to determine the size, quality, and quantity of PCR product. These parameters were used to verify PCR and prepare the appropriate dilutions for microarray printing. To verify the quality of the printing, microarrays are hybridized with labeled RNA similar to that used to make the EST library. Once the quality of the printing has been verified by hybridization, the availability of microarrays for ordering will be announced. The progress of each library can be followed in the Progress page.

Library tables provide searchable information on all samples in each library received from Stanford. Library tables include Stanford, EST database, and Genbank identifiers, the number of bases in the sequence submitted to Genbank, PCR product size and quality code (based on gel electrophoresis data), and information on which microarrays each sample is printed. For samples that are a part of the library but not printed, a code is provided indicating the reason for the sample's omission. The library table also provides the best BlastX entry for ESTs with excellent matches to known genes. Such information can be accessed by using the search table on the libraries page. Further description of the table variables can be found by clicking the information button at the bottom of the Libraries page.

Information on the microarray control sequences in our collection is provided in a searchable control table. The control table contains information including control gene location on each plate, gene name, plasmid name, vector name, primer, insert size, which lab generated such control and on which microarrays the control was printed. Please be sure to click the information button at the bottom of the Control Table page for more information.

Microarray element tables are provided for each microarray format used for printing. A search table allows you to quickly identify each printed spot by location and provide EST and BlastX identification. A complete microarray element table in text format can also be obtained for each microarray format used for printing using the search table. Further description of the procedures for probe preparation and printing and a detailed description of microarray formats can be found by clicking the information button at the bottom of the microarray element search page.

Microarray reproducibility data for each EST microarray produced can be found on the data page. Images of Microarrays hybridized with labeled targets derived from the same tissue used to make the EST library and graphical comparisons of hybridization signals and ratios between replicate spots and replicate slides are posted. Hybridization data from other experiments may also be posted. Signal intensity data in text format can also be obtained for each image.

An on-line order form and ordering instructions can be accessed from the ordering page. We will ship arrays once per month.

Standard protocols for labeling target RNA, hybridization, and other procedures can be found on the protocols page. Instructions for microarray users, preliminary data analysis information and other valuable tips on how to get started can be found here.

Some useful web resources on microarrays are posted on the links page.


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