title: FHCRC Arabidopsis Intergenic Array
status: Public on Aug 11 2005
contact.city: Seattle
contact.first: Ryan
contact.last: Basom
contact.state: WA
contact.address: 1100 Fairview Ave N
contact.country: USA
contact.institute: Fred Hutchinson Cancer Research Center
organism: Arabidopsis thaliana
manufacture_protocol: To obtain the 240 random single-copy loci, nonoverlapping 1-kb segments were selected at random from a database consisting of available contigs for A. thaliana chromosomes 1, 3, and 5 and complete chromosomes 2 and 4 from GenBank (August 2, 2000).  The Primer3 program running on a SUN Solaris workstation was applied with default settings to select 17-bp candidate primers with Tm > 50°C that encompass 700 ± 25 bp fragments. To stringently avoid redundant loci, each fragment was then searched against the database using blastn (word SIZE = 20, match SCORE = 1, mismatch SCORE = -50, gap open PENALTY = 50, gap extension PENALTY = 50, and no filtering), reporting only those hits with E value < 0.15, except for the first hit to itself.  Custom oligonucleotide primers were obtained in 96-well microtiter plates from MWG-Biotech and were used for PCR amplification with Ex-Taq polymerase (Fisher/Panvera Labs).  Microarrays were constructed by mechanically spotting PCR amplification products onto poly-lysine-coated microscope slides using an OmniGrid high-precision robotic gridder (GeneMachines). All loci were present in duplicate on the microarray.