EADGENE 24K Bovine oligonucleotide set
The Bovine array is constructed from the collection of Oligonucleotides designed by Christine Elsick and her team at Texas A&M. Initial selection of sequences for the design of the oligonucleotides was taken from the Bovine Oligo Microarray Consortium (BOMC) Database which contains 16,846 oligo sequences as well as the best Ensembl protein matches and Gene Ontology (GO) annotations for each sequence. http://www.bovineoligo.org. These sequences have been supplemented with 703 predicted RefSeq genes with no alignment to the bovine genome, 5943 reproductive tissue ESTs with a Bovine genome alignment but no protein alignment to the vertebrate protein list, and 508 positive and negative controls.
The final array has a total of 24,000 oligonucleotides which are printed in singlet. The oligos are 60 bases in length and there is one oligo per target sequence. The array is printed using an Arrayjet Supermarathon instrument onto Corning GAPS II slides. The DNA is cross linked to each slide and blocked using a BSA block. Each batch of slides is QC checked for the deposition of the oligonucleotides and a with test hybridisations using amplified RNA probes.
The arrays are prepared using the Bovine oligonucleotide consortium collection. Annotation for the genes on the array can be downloaded from www.bovineoligo.org.
EADGENE would like to stimulate the use of this tool by its partners, especially for the activities in the joint research program, to encourage data-exchange and comparison.