title: Cotton Fiber Oligonucleotide Microarray.V1
status: Public on Jun 10 2008
contact.city: Lubbock
contact.first: Thea
contact.middle: A
contact.last: Wilkins
contact.state: TX
contact.address: 2500 Broadway,Campus Box 42122
contact.department: Plant and Soil Sciences
contact.country: USA
contact.web_link: http://genomics.ttu.edu
contact.institute: Texas Tech University
organism: Gossypium arboreum
description: Cotton fiber ESTs were generated from 7-10 dpa fibers from the diploid species, Gossypium arboreum L. cv. AKA8401, at the Cotton Functional Genomic Center (CFGC) at the University of California-Davis (UCD) (cfgc.ucdavis.edu). A Unigene (UG)/Non-redundant (NR) set of 13,947 quality-controlled consensus sequences that define the cotton fiber transcriptome during rapid fiber elongation was assembled by Arpat et al 2004. The UG/NR set was used for designing oligonucleotide probes. A set of 12,227 Oligonucleotides (70-mer) were designed and synthesized by Operon Technologies (Operon, USA). Besides the cotton fiber oligos, the array comprised 71 experimental controls (positives, negatives, internals), transgene and vector controls, six spike-inn controls (Alien Spike mRNA, Stratagene), and blank and buffer controls spotted and replicated ≥ 2. Additional controls included cotton sequences deposited in GenBank, but not found in fiber dbEST.
manufacture_protocol: Oligonucleotides (oligoNT [70-mers]) were synthesized by Operon Technologies against 12,227 NR fiber ESTs. The cotton fiber microarray platform was fabricated, at CFGC-UCD, by spotting oligo NTs (40 um) in 50% DMSO in duplicates on Corning Ultra GAPS II microarray slides in 23 X 23 subarrays using the Omni Grid arrayer (Genomic Solutions) equipped with 16 (4X4) MicroQuill pins (Majer Precision Engineering).Post-printing processing of slides to chemically cross-link oligomers was performed according to the slide manufacturer’s instructions.