title: Porcine oligo micro array version 3
status: Public on Jan 16 2009
contact.city: Copenhagen
contact.first: Shila
contact.last: Mortensen
contact.email: shmo@vet.dtu.dk
contact.address: Bülowsvej 27
contact.department: Dep. for Veterinary Diagnostics and Research
contact.country: Denmark
contact.institute: National Veterinary Institute, Technical University of Denmark
contact.phone: +4572346000
organism: Sus scrofa
manufacture_protocol: The porcine oligo microarray version 3 (POM3) contains 192 porcine oligoes of maximum 75mer, targeting annotated mainly immune related porcine transcripts, a number of negative controls and spike in (Ambion).
  The porcine target sequences used for oligo design were obtained from public databases (NCBI, National Center for Biotechnology Information, GenBank (http://www.ncbi.nlm.nih.gov/) and TIGR, Institute for Genome Research, http://www.tigr.org/).
  Oligo design was performed using the microarray probe design software Oligowiz (Nielsen HB, Wernersson R and Knudsen S. Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays. Nucleic Acids Res 31: 3491-3496, 2003)(http://www.cbs.dtu.dk/services/OligoWiz2/), using the default settings, except for the oligo length, where longer oligos were selected.
  Oligos were synthesized and 5’ aminoallyl-conjugated by DNA Technology A/S (Århus, Denmark).
  Oligoes were diluted to 50mM in 50% DMSO -and array controls were diluted to 30mM in 50% DMSO. Oligoes were spottet on Corning UltraGAPSTM Coated Slides (Corning B.V.Life Sciences, Schiphol-Rijk. The Netherlands) using a VersArray ChipWriterTM Pro, software version 2.1.1 (Bio-Rad Laboratories Ltd. Ontario, Canada) equipped with 4 SMP3 pins (TeleChem International, Inc., Sunnyvale, CA).
  Oligos were spotted in triplicate in 4 sub-arrays each holding 12 x 15 spots and the 4 sub-arrays were repeated 3 times. After printing, slides were dried, UV cross-linked and stored in vacuum dessicator at room temperature until use. Prior to hybridization the slides were pre-hybridized according to manufacturer’s instruction.