title: US EPA Ecoarray FHM Pimephales promelas 10K 2000 gene (pilot) array
status: Public on Aug 21 2008
contact.city: Duluth
contact.first: Daniel
contact.middle: L.
contact.last: Villeneuve
contact.email: villeneuve.dan@epa.gov
contact.state: MN
contact.address: 6201 Congdon Blvd
contact.department: Mid-Continent Ecology Division
contact.country: USA
contact.institute: US EPA
organism: Pimephales promelas
manufacture_protocol: Briefly, probes for each gene were designed using Agilent’s probe design software.  Each of the 60-mer probes was synthesized in situ on 1” x 3” (24.2 mm x 76.2 mm) treated glass slides using SurePrint inkjet deposition technology (http://www.chem.agilent.com).  All probes were synthesized in duplicate at random locations on the slide surface.  Since we could not confirm the direction of genes with an E-value greater than 1E-5, probes were designed and synthesized from both strands (forward and reverse complement) for the sequences.  To facilitate evaluations of the microarray (described below), multiple probes that spanned the vitellogenin (vtg) 1 genes were also synthesized on the chips.  Probe sequences for each of the genes are available (under license agreement) from EcoArray.  Probes for specific genes on the microarrays were assigned a unique Probe Identification number, similar in concept to Accession numbers that are assigned to sequences in National Center for Biotechnology Information databases.  This number (EA_Pp_###) allows for the cross-referencing of sequences from one experiment.