title: Tiling microarray OS16975 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 3
status: Public on Feb 21 2007
contact.city: New Haven
contact.first: Rajkumar
contact.last: Sasidharan
contact.email: rajkumar.sasidharan@yale.edu
contact.state: CT
contact.address: 266 Whitney Avenue
contact.department: MB & B
contact.country: USA
contact.institute: Yale University
organism: Oryza sativa
description: This experiment was designed to identify transcribed regions of japonica subspecies of the rice genome. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of all the 12 chromosomes were designed to measure genome-wide transcription. A total of 12253842 36mer oligonucleotide probes positioned every 46 nt on average were used for this purpose. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA population (seedling root, seedling shoot, panicle, and suspension cultured cells).
manufacture_protocol: Microarrays containing these oligos are synthesized on glass with Expedite DNA synthesizers (Applied Biosystems, Foster City, CA) in conjunction with Maskless Array Synthesis units (NimbleGen Systems, Madison, WI).