title: DJF Pig 55K v1
status: Public on Jan 11 2008
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: DIAS_PIG_55K4_v1 consists of 55.548 features: 26.877 PCR products amplified from cDNA clones and 867 control features spotted as neighbor duplicates in a 4 x 12 array with sub-arrays each consisting of 34 x 34 spots.
  The cDNA clones were selected from the cDNA libraries generated in the Sino-Danish Pig Genome Sequencing Consortium using BLASTN sequence similarity (P ≤ 10-8) such that the cDNAs covered the largest possible number of human gene transcripts in NCBI’s RefSeq database, release 15. To represent previously uncharacterized genes and candidate porcine specific genes we added cDNAs to the selection list, for which their EST clusters, of minimum depth 3, showed limited or no similarity to any known mammalian gene transcripts. The selected clones were rearrayed from the libraries using a QPixII (Genetix), amplified by PCR and purified using the 384 well Microarray PCR Purification Kit (Telechem International). The PCR products were evaluated by agarose gels and dried by speed vac and resuspended in spotting solution. The control features consists of positive spots (also known as “landing lights”), blanks (spotting buffer) and selected spots from the Lucidea Universal ScoreCard (GE Healthcare) which contains both intensity dilution series and different ratios. The positive spot was prepared by PCR amplification of a bovine EST fragment using a dNTP mix containing amino allyl-dUTP followed by labeling with Alexa-488, -555, -594 and -647. The arrays were spotted on UltraGAPS slides (Corning Incorporated) at 20 C/55 % RH using an SDDC-2 MicroArrayer (BioRad) with 48 x 946 MP2.5 pins (Telechem International) with DNA resuspended in Micro Spotting Solution Plus (Telechem International). Slides were dried and UV cross-linked (300 mJ) and stored in a vacuum desiccator until use.
  
  The sequences of the cDNA clones can be found in the attached file "GPL6173_array_cDNA_28k_2005-07-13.cDNA.scr.zip". The attached .gal file contains the original annotation, but an updated version of the annotations have been obtained by blast against mammalian refseq (version 34, file: "GPL6173_p55k-vs-mam-refseq34-2009-04-17.txt") and against Human refseq (release 2009-03-09, file: "GPL6173_p55k-vs-hsa-refseq-2009-04-17.txt") (Rank = 1, Minimum alignment length = 50, Minimum percent alignment = 85 %). An annotation package (file: GPL6173_55k3Ver2HsRs20090309AL50PA85_1.0.zip") has furthermore been built in R (version 2.8.0) using AnnBuilder (version 1.20.0).