title: Galbraith Lab Arabidopsis 29K v3.0
status: Public on Sep 05 2007
contact.city: Blacksburg
contact.first: Andy
contact.last: Pereira
contact.email: pereiraa@vbi.vt.edu
contact.state: VA
contact.address: Washington Street MC0477
contact.department: Virginia Bioinformatics Institute
contact.country: USA
contact.institute: Virginia Tech
contact.phone: 540-231-3784
organism: Arabidopsis thaliana
manufacture_protocol: The long oligonucleotide 70-mer Operon array spotted in David Galbraith's Laboratory, comprising 29,000 genes of Arabidopsis were used.
  The Arabidopsis thaliana AROS V3.0 contains 29,110 longmer probes and represents 26,173 protein-coding genes, 28,964 protein-coding gene transcripts, and 87 microRNA genes from Arabidopsis thaliana.
  Pseudogenes are excluded from this oligo design which is based on the ATH1 release 5.0 of the TIGR Arabidopsis genome annotation database and release 4.0 of the miRNA Registry at the Sanger Institute and allows detection of alternative splicing variants using common, partial common, or individual transcript oligos.
  All probes are Tm normalized to 78ºC (±5ºC) and have a 5' amino linker.
  The oligonucelotide probes were spotted onto slides at the Galbraith lab following the protocol described.
  15 mL of 3XSSC were added to each well of the 300 pM oligonucleotide set to make a 20 microM oligonucleotide solution.
  These were transferred onto an orbital shaker for 1 h at RT at 100 rpm and used for printing.
  The Arabidopsis oligonucleotide microarrays are printed on aminosilane-coated "Superamine" slides (Telechem) or "Powermatrix" slides (Full Moon Biosystems), using Telechem Type SMP3 printing pins.
  The printing conditions used are: Single array element printed per oligonucleotide, 48 pins in the print head, 31% relative humidity, redipping after every 50 slides.
  The print head Z- velocity is set to a maximum of 10 mm/sec.
  The slides are then baked for 2h at 80oC, and stored dry and in darkness at RT prior to use.