title: ViaLactia Biosciences custom bovine array 22k version 1b
status: Public on Jun 30 2009
contact.city: Auckland
contact.first: Matt
contact.middle: D
contact.last: Littlejohn
contact.email: matt.littlejohn@vialactia.com
contact.address: PO Box 109-185 Newmarket
contact.country: New Zealand
contact.institute: DairyNZ
contact.phone: +64 9 589 4572
organism: Bos taurus
description: This array is an early version of the now commercially available Agilent Bos taurus 44k array (Agilent design ID 015354).
manufacture_protocol: 325,000 EST, mRNA, and CDS region sequences for Bos taurus genes were retrieved from GenBank, and supplemented with paired 5'- and 3'-reads from 100,000 ESTs obtained from normalized bovine fetal brain, lactating and non-lactating mammary gland cDNA libraries. After repeat masking, sequences were clustered by pairwise-comparison using Paracel Transcript Assembler (Paracel, Pasadena, CA, USA) to reduce redundancy, and the resulting clusters were mapped to genes predicted from the 2.1 assembly of the bovine genome. Gene-specific cluster sequences were then supplemented with novel transcript sequences predicted by the NCBI RefSeq project (http://www.ncbi.nlm.nih.gov/RefSeq/). Probe sequences (60-mer) targeted towards the 3' regions of the transcripts were designed by Agilent Technologies. 21,495 unique probe sequences were selected for array manufacture by in-situ synthesis.