Maize Oligonucleotide Array Factsheet
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
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
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
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. Jaroslav Janda (email@example.com).
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
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).
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.
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 Georgina Lambert (firstname.lastname@example.org)
for questions regarding microarray orders.
Last modified: April 1, 2008Thursday, 18-Jun-2009 14:58:44 MST