title: Chen Lab Cotton 25k oligo array
status: Public on Dec 01 2008
contact.city: Austin
contact.first: Z Jeffrey
contact.middle: Jeffrey
contact.last: Chen
contact.email: zjchen@austin.utexas.edu
contact.state: TX
contact.address: 2506 Speedway NMS 3.122 Stop A500
contact.department: Molecular Biosciences
contact.country: USA
contact.institute: The University of Texas at Austin
contact.phone: 512-475-9327
organism: Gossypium hirsutum
description: Used in the study 'Transcriptional and functional analyses of fiber genes in cotton.'
manufacture_protocol: The first set of 1,536 oligonucleotide probes was designed from a pilot set of cotton microarray in the previous work (Lee et al., 2006). The second set of 12,006 oligonucleotide was designed from an exemplar sequence set which was chosen from a clustere set of unigenes by single-linkage clustering with BLASTN using Picky v1.0 (Chou et al., 2004; Udall et al., 2006; Udall et al., 2007). The 12,006 oligonucleotide probes include genes encoding a large number of transcription factors, and several thousand genes that had homology to Arabidopsis genes (Udall et al., 2007). The third set of 9,629 oligonucleotides probes was designed from CGI8 (http://compbio.dfci. harvard.edu/tgi) that contained 55,673 unique sequences using Picky v2.0. This GH_TMO ESTs showed the accumulation of genes encoding putative transcription factors such as MYB and WRKY and genes encoding predicted proteins involved in auxin, brassinosteroid (BR), gibberellic acid (GA), abscisic acid (ABA) and ethylene signaling pathways (Yang et al., 2006). The probes that target the same genes as in the first two probe sets were excluded in the third set. This large set of cotton oligonucleotide microarray may include about 46–60% of the total genic diversity and most of the probes had a single target (Udall et al., 2007).