Maize Oligonucleotide Array Project

Maize Oligonucleotide Array Project

Maize Oligonucleotide Array Factsheet

Overview

Please take a few minutes to read this long oligo array information sheet. You have invested both time and money in planning your microarray experiment and the information provided on this sheet could be critical to making your microarray experiment a success.

Microarray Storage and Hybridization Preparation

Make sure that you have received the right slides that you requested.

Store the microarrays at room temperature protected from light in a dust free environment. Do not store arrays in the cold room or above 50 °C.

Long-oligo arrays can be stored up to 12 months at room temperature. Do not forget the re-hydration and UV crosslinking steps that are needed prior to hybridization.

The DNA oligos are printed on the labeled side of the slide. When exposing the slides to either the water vapor for the re-hydration or UV light for crosslinking, be sure to expose the DNA side of the slide.

At no time before the crosslinking step are the slides to be immersed in water. Slides may be stored for longer periods of time after re-hydration and UV crosslinking.

Microarray Hybridization Protocols

We strongly suggest that you use the optimized RNA labeling and hybridization protocols which are available in the Protocols section at www.maizearray.org/maize_protocols.shtml. These protocols have been extensively tested for both salt and temperature conditions using a variety of statistical criteria which measure reproducibility between replicates and spurious cross-hybridization. If you have any question regarding the protocol feel free to contact Dr. Roger Barthelson (rogerab@cals.arizona.edu).

Image Processing Files

After hybridization it is recommended to scan the slides immediately; however the slides can be stored in a light protected dust free environment for few days without losing much of the signal (Photo bleaching is a important factor that causes significant reduction in the hybridization signal. Therefore it is advised not to expose the microarray slides directly to bright light after hybridization).

You may want to consider scanning your slides at multiple scanner settings. Some groups have reported enhanced ability to detect small changes in genes that are either weakly or strongly expressed using scanner settings that are either higher or lower that the optimal setting.

Many of the present day microarray scanners use .GAL files for spot finding. You can download these files from our website (www.maizearray.org/maize_annotation.shtml). Since other programs may require formats different from GAL files, we also post an Excel spreadsheet containing all the information that is needed for spot finding.

Availability of Oligo Sequences

The oligo sequences are available from Operon Biotechnogies (formerly Qiagen/Operon) at http://omad.operon.com/download/index.php. Winzip is required to decompress the files.

Microarray Payment

A payment invoice is included with your microarrays. Payment for microarrays is due upon receipt and can be made by credit card, check, money order, or wire transfer. Due to the cost recovery system which supports the production of future arrays, we will be unable to process array orders for those laboratories that have outstanding invoices from prior orders. Please contact Dr. Roger Barthelson (rogerab@cals.arizona.edu) for questions regarding microarray orders.

Last modified: April 1, 2008Thursday, 15-May-2008 09:10:30 MST