title: EcoArray Fathead minnow 44K v1.0
status: Public on Sep 16 2008
contact.city: Alachua
contact.first: Barbara
contact.middle: Joan
contact.last: Carter
contact.email: bcarter@appliedfoodtechnologies.com
contact.state: FL
contact.address: 12085 Research Drive
contact.department: R&D
contact.country: USA
contact.institute: Applied Food Technologies
organism: Pimephales promelas
description: Our fathead minnow(FHM) microarray was constructed by first compiling all known gene sequences for fathead minnows: 250,000 ESTs published by the JGI plus our own proprietary sequences obtained from suppression subtractive hybridizations and normalized library construction. We then assembled these genes to discern ~47,000 non-overlapping unique sequences (contigs and singlets). Homology searches (Blast) were performed on these sequences in order to provide annotation (gene name) and ontology (gene function) information where present. A total of 21,495 contigs were assembled. Probes were designed using Agilent’s web-based E-Array program.
  The content of our FHM microarray is located on our web site and contains 21,495 contigs (probes spotted in duplicate) of which:
  • 17,588 are annotated and represented by one sense or antisense probe.
  • 1,331 are annotated and represented by one reverse complement for the probe.
  • 2,576 are poorly annotated (e-value >0.0001) and represented by one probe.
manufacture_protocol: EcoArray selected Agilent Technologies as the manufacturer of our microarrays for environmental toxicology. Agilent uses SurePrint inkjet deposition of in situ synthesized 60-mer oligonucleotides and superior quality 1” x 3” (24.2 mm x 76.2 mm) treated glass slides for overall excellent performance of their microarrays. This process minimizes variability across each production lot (batch to batch) and provides the highest consistency in slide-to-slide comparisons. These glass slide microarrays are designed for either a one- or two-color (cyanine-3 and cyanine-5) labeling reaction, the most reliable and sensitive methods for detecting differentially expressed genes. Agilent’s Feature Extraction software, when used with a high-resolution (5μm) scanner, provides QA metrics for each individual microarray, ensuring quality results.  Each slide contains four individual 44K arrays.