title: [Barley1] Affymetrix Barley Genome Array
status: Public on Jul 09 2004
contact.city: Santa Clara
contact.last: Affymetrix
contact.email: geo@ncbi.nlm.nih.gov, support@affymetrix.com
contact.state: CA
contact.country: USA
contact.web_link: http://www.affymetrix.com/index.affx
contact.institute: Affymetrix, Inc.
contact.phone: 888-362-2447
organism: Hordeum vulgare
description: Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html
  
  The GeneChip Barley Genome Array was designed and funded by the USDA-IFAFS Triticeae Improvement group (R. Wise, T. Close, G. Muehlbauer, R. Wing, and A. Kleinhofs) in collaboration with Affymetrix and the international barley community. A community effort resulted in a significant improvement to sequence quality through better clustering and derived annotations.
  
  Sequences used for the Barley Genome Array design were collected from consortia labs submitting EST sequences and by collecting sequences from the NCBI/GenBank non-redundant database. Approximately 400,000 raw barley ESTs were submitted from 84 libraries, and about 350,000 survived quality pruning.
  
  Stringent CAP3 clustering (-p95 -d60 -f100 -h50) was performed and resulted in 53,030 "unigenes" (26,634 contigs and 26,396 singletons). 25,500 contigs and singletons had complete 3' ends suitable for array design (see HarvEST Triticeae v0.95 and higher). This included all 1,145 known barley genes (including alleles) from the NCBI non-redundant database. The nonredundant cloned gene set was integrated with the EST clusters to aid in scaffolding the ESTs and also to retrieve any rare interesting genes (e.g., Mla, Rar1, Sgt1, Rpg1) for inclusion on the GeneChip microarray. After pruning against an enhanced Triticeae repeat element database (TREP), the exemplar set of 25,500 contigs and singletons was submitted to Affymetrix for initial computation.
  
  Potential applications for the barley array include analysis of malting properties, pest and disease control, abiotic stress tolerance, nutritional characteristics, and reproductive development. The GeneChip Barley Genome Array was released in June, 2003.
  
  Annotations derived from Affymetrix CSV file dated 6/23/2004
manufacture_protocol: see manufacturer's web site