title: Cotton_oligonucleotide_array_v1.0
status: Public on Sep 14 2006
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 hirsutum
  Gossypium arboreum
  Gossypium raimondii
description: Comment:  On this platform, we have not distinguished which features were specifically designed from each of the three different Gossypium species because all probes were designed from a single assembly of Gossypium ESTs.  An effort to do so, may have been misleading since all probes are expected to hybridize equally well to homologs in all three species due to their limited coding sequence divergence.
  Supplementary information about this platform can be obtained at http://cottonevolution.info/microarray.
  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 the 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: After oligo design at Iowa State University, one set of oligonucleotides (12,006) were synthesized and aliquoted into 3 replicate plates of 1000 pmoles by IDT Technologies (Coralville, IA, USA).  An earlier set of oligonucleotides was synthesized for microarray development in the Chen lab at Texas A&M University.  An aliquot of 384-well plates from both sets of oligonucleotides was hydrated in water and diluted to the printing concentration with 3X SSC.  Two spots of each oligo from the same pin-dip were printed in separate slide sections on Corning epoxy slides 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 the print batch were checked using SpotCheck (Genetix).  Printed cotton microarrays are publicly available at http://cottonevolution.info.