title: EcoArray 8 x 15K Daphnia magna Microarray v1.0
status: Public on Sep 27 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: Daphnia magna
description: Our Daphnia microarray was constructed by first assembling sequence from publicly held accessible databases1 to identify non-overlapping, unique sequences (singlets and contigs). 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 4,936 contigs were assembled. Probes, 60- bases in length, were designed using Agilent’s web-based E-Array program. The content of our Daphnia microarray is located on our web site and contains 4936 contigs of which:
  • 2,255 are annotated and represented by one probe for the forward strand.
  • 247 are annotated and represented by one reverse complement for the probe.
  • 2,434 are un-annotated and represented by one sense and one antisense probe.
  Thus, we designed a total of 7,370 probes; each spotted twice on the array.
manufacture_protocol: These microarrays are manufactured for EcoArray by Agilent Technologies, Inc. in an “8-pack” (8 individual 15K arrays per slide) format, which allows for maximum information at lowest cost. Each of the arrays on the slide may be hybridized with a unique sample. Probes are synthesized in situ using Agilent’s inkjet based “SurePrint” technology. These arrays are manufactured on superior quality 1” x 3” (24.2 mm x 76.2 mm) treated glass slides for overall excellent performance. This process minimizes variability across each production lot (batch to batch) and provides the highest consistency in slide-to-slide comparisons. See website for details: http://www.agilent.com