title: Operon Pig 14.4K genome microarray v1.0.2
status: Public on Jul 28 2010
contact.city: Edmonton
contact.first: James
contact.middle: Michael
contact.last: Wilkinson
contact.email: jamiewilkinson@hotmail.com
contact.state: Alberta
contact.address: Ag/For Building
contact.department: Agriculture, Food, and Nutritional Science
contact.country: Canada
contact.institute: University of Alberta
organism: Sus scrofa
manufacture_protocol: The Operon pig genome oligo set contains 10,665 70-mer probes with a hit to a known human, mouse, and pig gene transcript and some sequences containing a 3' EST. The pig genome oligo extension set contains 2,632 70-mer probes rpepresenting 2,632 gene sequences with at least one 3' EST. In total, 13,297 pig probes are included on the array (IDs start SS0). All probes were designed from The Institute of Genome Research (TIGR) Sus scrofa Gene Index (SsGI) version 5.0, released on October 1st 2002. All Transcript Consensus (TC) sequences and singleton expressed transcripts (ETs) were aligned using BLAST to known human, mouse, and pig genes. All TCs and singleton ETs with a more than 75% homology over at least 100 bases to a known human, mouse, or pig transcript and yielding a designed probe of less than or equal to 70% cross hybridization identity was included in the set. All probes were designed from the sense strand. They were also designed to have a Tm of 78°C +/- 5°C, be within 1,000 bases from the 3' end of the transcript, not have any contigous single base repeat of more than 8 bases in length, not have a potential hairpin structure with a stem length of more than 9 bases, and not have more than 20 contigous bases common to any other gene. All the component ESTs used to make the TCs were obtained from Genbank. All ESTs with the keyword 3', denoting a 3' EST, were marked and oligos designed in the same way. In addition to these pig probes, various negative controls are also included on the array. These include 10 sequences from the SpotReport Alien cDNA validation System from Stratagene (sequences designed to have no sequence homology to other genomes - IDs start Alien), 7 randomized probe sequences and 4 genes from the plant Arabidopsis thaliana (IDs start SSN), and 13 sequences from bacteria or viruses (from Affymetrix synthetic microarray sequences - IDs start NC). Probes were contact printed on glass aminosilane coated slides (Schott Nexterion) using a arraying robot and a 48 pin tool. Each subgrid on the array contains spots in a 24 row by 25 column grid. The top 12 rows in each subgrid are a repeat of the bottom 12.