title: Rat 2K Array
status: Public on Jan 26 2005
contact.city: Milwaukee
contact.first: David
contact.middle: P.
contact.last: Basile
contact.email: dbasile@mcw.edu
contact.state: WI
contact.address: 8701 Watertown Plank
contact.department: Physiology
contact.country: USA
contact.institute: Medical College of Wisconsin
contact.phone: 414-456-8785
organism: Rattus norvegicus
description: The custom microarrays were manufactured by the Department of Physiology at the Medical College of Wisconsin. Microarrays were printed with a GMS 417 robotic arrayer from Affymetrix (made by Genetic Microsystems) that has a printhead with 4 pin-and-ring print tips.  Arrays were prepared from the first 18 of 88 plates of a rat cDNA library from Research Genetics.  The clone set represents 1631 known genes and 192 ESTs. We included 506 negative control spots and 456 positive control spots.  Following amplification, PCR amplicons were distributed into 384-well polypropylene plates (Genetix, 384 micro array), resuspended in 50% DMSO and printed onto poly-L-lysine coated glass slides.  Print configuration is 8 blocks in a 2 x 4 arrangement. Positive controls were printed in each block, and included beta-actin and GAPDH.  Negative controls were also printed in each block, and included 5 Arabidopsis gene fragments, mouse COT-1, DMSO, poly dA, yeast tRNA, and PCR buffer with and without primers. The microarray spot density is 250 microns (center-to-center).  Spot diameters are approximately 120-150 microns.  After printing, DNA was cross-linked to the slides by UV irradiation at 65 mJ (Stratalinker UV Crosslinker, Stratagene).  The microarrays were post-processed according to the procedures on the Stanford website (http://cmgm.stanford.edu/pbrown/protocols/index.html) and subsequently stored at room temperature in a desiccated chamber until use.
  
  