title: ARK-Genomics G. gallus 20K v1.0
status: Public on Jul 11 2007
contact.city: Roslin
contact.first: Mark
contact.last: Fell
contact.email: mark.fell@bbsrc.ac.uk
contact.state: Midlothian
contact.address: Roslin Institute
contact.department: Bioinformatics
contact.country: United Kingdom
contact.institute: ARK-Genomics@Roslin Institute
organism: Gallus gallus
description: This is an oligo array containing 20460 elements. Oligos were designed using gene predictions from Ensembl and TIGR, together with full-length cDNAs from the BBSRC UMIST ChickEST database (http://chick.umist.ac.uk/) and chicken bursal EST sequences from Jean-Marie Buerstedde's DT40 database. Sequences from these resources were aligned together and oligos were designed against regions in common to more than one dataset. Oligos were then designed using OligoArray2.0.
manufacture_protocol: Oligos were resuspended in Corning Pronto Epoxide spotting solution to
  give a final concentration of 20uM. DNA was printed on Corning Epoxide
  slides using a Genomic Solutions MicroGrid II arrayer and the MicroSpot
  10K pins, according to manufacturer's instructions. All printing was
  carried out in conditions of constant humidity (52% RH) and temperature
  (20C) in a room supplied with HEPA filtered air. Prior to printing the
  pins were cleaned by ultra-sonication in water and if necessary 50mM
  potassium hydroxide. A test print of all pins was carried out by
  printing Cy3 streptavidin conjugate dye in printing buffer onto epoxide
  slides and printing 100 features per pin. When all pins were printing
  consistent size spots for more than 80 features they were accepted as
  ready to print. The MicroGrid II was then programmed for the array print
  run, with a grid layout file prepared to allow duplicate printing at
  random within a patch. At the end of the print run the slides were
  removed following the program instructions in preparation for post
  processing.
  Slides dessicated overnight and then transferred to a humid chamber (45%
  humidity, 42C) for 8 hours. The slides were then washed in 0.2% SDS
  (room temperature) for 2 minutes with agitation before being rinsed in
  three water washes (30seconds, 30 seconds, 1 minute) with agitation.
  After these steps the slides were then incubated in water at 50C for 20
  minutes before spin drying. The slides were then stored in a desiccator
  in the dark ready for use.