title: Cotton_oligonucleotide_array_v2.0
status: Public on Feb 06 2007
contact.city: Athens
contact.first: Alan
contact.middle: R
contact.last: Gingle
contact.email: agingle@uga.edu
contact.state: GA
contact.address: 111 Riverbend Rd.
contact.department: Center for Applied Genetics Technologies
contact.country: USA
contact.institute: University of Georgia
organism: Gossypium barbadense
  Gossypium hirsutum
  Gossypium arboreum
  Gossypium raimondii
description: Comment:  This is the second version of the cotton nucleotide platform. Three independently designed sets of IDT (Coralville, IA, USA) oligonucleotides are included on this microarray platform.  The first set of 1,152 oligonulceotides were designed by the Chen lab formerly located at Texas A&M.  A second set of 12,006 oligonucleotides was designed by the Wendel lab located at Iowa State University.  The third set of oligonucleotides (9,629) was designed by The Institute for Genomic Research (TIGR) in collaboration with the Chen Lab at The University of Texas using the latest TIGR cotton EST assembly (CGI8).  Version 1 (GEO#  GPL4305) included dual spotted oligonucleotides from only the first two sets of oligonucleotides.  We have not distinguished which features were specifically designed from each of the different Gossypium species because all probes were designed from an assembly of Gossypium ESTs.  An effort to do so may have been misleading, since all probes are expected to hybridize equally well to homologs across the different species, due to their limited coding sequence divergence.
  The oligo probes have been annotated with GenBank accession identifiers based on any one of the following criteria.
  1) GB_ACC: A probe was specifically designed to target a particular mRNA with associated GenBank accession identifier.
  2) GB_LIST1: A high quality alignment (length >= 60 and percent identities >= 92%) to a member of either the ESTother or nt databases.
  3) GB_LIST2: A high quality alignment (length >= 60 and percent identities >= 92%) to a contig member of the estinformatics (http://www.estinformatics.org/) assembly for Gossypium (assembly date: 12/31/2006).  These annotations are based on EST membership in the aligned contig and not on direct high quality alignment to any member EST.  Therefore, the number of associated accessions can be quite large.
  A number of probes failed to meet any of these criteria and, therefore, have not been annotated with GenBank accession identifiers.  However, their available information can be accessed at http://cottonevolution.info/microarray.
manufacture_protocol: An aliquot of 384-well plates from all three sets (see description) of oligonucleotides was hydrated in water and diluted to the printing concentration with 3X SSC.  A single spot of each oligo from a single pin-dip was printed on each Corning epoxy slide at the Washington University Microarray Core facility using a locally constructed linear servo arrayer (after the DeRisi model, http://derisilabs.ucsf.edu/).  After printing, slides were allowed to dry in 50-70% humidity for 12-16 hrs at room temperature and subsequently cross-linked at 150 mJoules in a Strata-linker (Stratagene, Inc., La Jolla, CA, USA).  Two slides from each print batch are assessed for quality using SpotCheck (Genetix).  Batches of printed cotton microarrays and associated quality data are publicly available at http://cottonevolution.info.