title: Maize Pioneer Hi-Bred 105K mRNA Microarray
status: Public on Sep 02 2010
contact.city: Johnston
contact.first: Kevin
contact.middle: Robert
contact.last: Hayes
contact.email: kevin.hayes@pioneer.com
contact.state: IA
contact.address: 7200 NW 62nd Ave
contact.country: USA
contact.institute: Pioneer Hi-Bred International
organism: Zea mays
description: The Agilent “105K” microarray chip was designed for maize genomic and transcript sequences in an effort to cover most maize genes with at least one 60-mer oligonucleotide probe.  A pool of about 1.4 million public and private ESTs was consulted, derived from diverse tissues and treatments. The majority of the sequences was derived from the B73 genotype, but there were other genotypes represented.  A higher quality subset of 1.1 million ESTs was used to generate a transitory transcript assembly of about 66K transcript sequences of average length 1.0 kb.  At least one 60-mer oligo was designed for nearly all of these transcripts, but at times more than one oligo was designed per transcript.  In an effort to identify other genes, or perhaps parts of genes, not represented in the 66K transcript set, and to fill out the array, various BLAST analyses were conducted against the then (in fall 2006) available public B73 genomic sequences, namely B73 BACs in GenBank and the AZM5 GSS Assembly dataset produced by TIGR.  The resulting array design is believed to encompass most maize genes at least once, but there are certainly genes missing, others represented more than once, and sequence errors or genotypic variation in the dataset, or oligos designed to straddling intron-exon junctions, or to chimeric junctions inherent in ESTs and their assemblies, that may deter some oligos from functioning against a B73-specific transcript sample.  Subsequent efforts to estimate the number of unique genes in this microarray suggest about 45,000 genes.  This “105K” format Agilent microarray consists of 103,685 oligos designed to maize genic sequences. The balance of the space on the “105K” microarray (105,073 total oligos) was reserved for technical and internal hybridization controls.
manufacture_protocol: Produced by:
  Agilent Technologies Inc.
  5301 Stevens Creek Blvd
  Santa Clara CA 95051
  United States