Honey Bee Oligonucleotide Microarray

Long oligos for the array were developed by Debashis Rana and Gos Micklem, http://www.gen.cam.ac.uk/Research/micklem.htm at Cambridge University, using a modified version of OligoArray 2.1 in an iterative process to identify unique sequences (60-69mers) each of the bee genes identified by the honey bee genome project "official gene set". The set of oligos was selected to have as tight a melting temperature distribution as possible, and to avoid repetitive sequences and other anomalies. A total of 12,915 unique oligos were generated representing all but three of the 13,145 source sequences used (details on source sequences, which encompassed honey bee predicted genes, EST’s and markers for bee parasites and pathogens available at:http://file-server.igb.uiuc.edu/GBB/). The discrepancy in source sequence versus oligo counts reflects oligos matching 2 or more source sequences (mainly though redundancies in the Official Gene Set). Reverse-strand oligos were added for 525 predictions, focusing on EST reads and transcripts predicted for bee pathogens (Table 2 in file ArrayDevelopment.rtf at).  As such, the final set contains 13,440 oligos (sequences in Array_fasta/Oligoset13440.txt at the above web site). The design process was similar to that of the INDAC long oligo set designed for the fruit fly Drosophila melanogaster and available at: http://www.flymine.org/release-5.0/aspect.do?name=INDAC and http://www.flychip.org.uk/services/core/FL002.

References:
Design Method:

Kreil DP, Sykacek P, Auburn RP, Meadows LA, Russell RR, Fischer B, Matilla SS, Rana D, Russell S, Micklem G. INDAC microarray probe design, validation and calibration experiments. Genome Research, submitted

FlyMine database:

Lyne R, Smith R, Rutherford K, Wakeling M, Riley T, Guillier F, Ji W, Mclaren P, Woodbridge M, Janssens H, Watkins X, Rana D, Varley A, Lilley K, Russell S, Ashburner M, Mizuguchi K, and Micklem G. FlyMine: An Integrated database for Drosophila and Anopheles genomics. Genome Research, submitted

Design Method

Kreil DP, Sykacek P, Auburn RP, Meadows LA, Russell RR, Fischer B, Matilla SS, Rana D, Russell S, Micklem G. microarray probe design, validation and calibration experiments. Genome Biology , submitted

README - Honey bee array development files

Information on the sequences represented on the array can be found
at:  http://file-server.igb.uiuc.edu/GBB/.  These folders contain
files describing the development of the array in more detail
(ArrayDevelopment.rtf) and subfolders with 1) array sequence
information (Array_fasta) and 2) connections between array features,
source sequences, the honey bee genome assembly, and the Drosophila
melanogaster genome (Array_analysis subfolder).

 The oligo array accession file has been posted on ArrayExpress' website (A-MEXP-755). 
Follow this link to view the file and supporting documentation.
http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-MEXP-755

Funding for oligo design and synthesis and array validation provided by National Research Initiative grant AG2004-36504-14277 from the USDA (G.E. Robinson, PI, M. Band, J.D. Evans, G. deGrandi Hoffman, K.P. White, Co-PIs)