title: DIAS_PIG_27K2_v2
status: Public on May 23 2006
contact.city: Tjele
contact.first: Jakob
contact.last: Hedegaard
contact.email: Jakob.Hedegaard@ki.au.dk
contact.address: PO-box 50
contact.department: Department of Genetics and Biotechnology
contact.country: Denmark
contact.institute: Aarhus University, Faculty of Agricultural Sciences
contact.phone: (+45)89991363
organism: Sus scrofa
manufacture_protocol: The DIAS_PIG_27K2_v2 array consists of 27.648 features: 5.375 PCR products amplified from cDNA clones, 985 control features and 552 oligonucleotides spotted as quadruplicates. The array consists of 4 x 12 sub arrays each of 24 x 24 spots. The four replicated spots were spotted pair wise on different locations on the slide. Practically, the 6.912 elements were first spotted twice in 2 x 12 sub arrays (sub array-column 3 and 4). The source plates were then rotated 180 ° and the final 2 x 12 sub arrays (sub array-column 1 and 2) were spotted.
  The cDNA clones used as template were selected from the cDNA libraries generated in the Sino-Danish Pig Genome Sequencing Consortium (Gorodkin et al.: Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 ESTs. Genome Biol 2007, 8:R45). The cDNA clones were selected by blasting the human sequences of genes of interest for similarity (P ≤ 10-8) to members of the porcine EST selection at DIAS. Furthermore, a number of clones were selected from lung, liver and muscle Longissimus dorsii cDNA libraries to represent major clusters of EST sequences.
  The control features consists of dilution series of selected clones and oligonucleotides, genomic DNA from pig and salmon, sheared pig and salmon genomic DNA, ds cDNA from pig lung and muscle, different porcine C0t DNA fractions and blanks.
  The 552 oligonucleotides (70-mer) were designed from the sequence of p450 related genes using the SEPON software (Hornshøj et al, “SEPON, a Selection and Evaluation Pipeline for OligoNucleotides based on ESTs with a non-target Tm algorithm for reducing cross-hybridization in microarray gene expression experiments”, Bioinformatics. 2004 Feb 12;20(3):428-9).
  The arrays were spotted on UltraGAPS slides (Corning Incorporated) at 20 C/55 % RH using an SDDC-2 MicroArrayer (BioRad) with 24 SMP3 stealth pins (Telechem International) with DNA resuspended in Micro Spotting Solution (Telechem International). Slides were dried and UV cross-linked (300 mJ) and stored in a vacuum desiccator until use.