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GeneChip Barley Genome Array

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.

Part # Description Unit Size Your Price (USD)
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900515
GeneChip Barley Genome Array
contains 6 arrays    Please Inquire
     

This GeneChip array is available through the Affymetrix Made-to-Order Program, which enables you to purchase selected custom array designs and previous-generation GeneChip arrays no longer available as catalog products. Learn more about ordering and support of GeneChip Made-to-Order arrays.

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. Annotation is available in NetAffix Data Analysis Center and from HarvEST.

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.

Visit BarleyBase, a USDA-funded public repository for plant microarray data.

For research use only. Not for use in diagnostic procedures.

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Data Sheets

Made-to-Order Program (pdf, 144 KB)

Library Files

Barley Genome Array (zip, 12 MB)

Manuals

Expression Analysis Technical Manual, with Specific Protocols for Use with the Hybridization, Wash, and Stain Kit (pdf, 1.70 MB)

Probe Set Data in MAGE-ML Format

3' IVT Express Kit User Manual (pdf, 1.6 MB)

HT 3' IVT Express Kit (pdf 5.93 MB)

Package Inserts

Barley Array (pdf, 112 KB)

Protocol, Long

Gene Expression Arrays

Other

Fluidics Scripts

NetAffx Annotation Files

Barley1 Annotations, CSV format, Release 31 (1 MB 08/11/10)

Barley1 BLASTP annotations, CSV Format, Release 32 (2 KB 06/09/11)

Barley1 Annotations, MAGE-ML XML Format, Release 31 (15 MB 08/11/10)

Barley1 Annotations, MAGE-ML XML Format, Release 32 (15 MB 06/09/11)

Barley1 BLASTP annotations, CSV Format, Release 31 (5 KB 08/11/10)

Barley1 Annotations, CSV format, Release 30 (1 MB 11/15/09)

Barley1 Annotations, MAGE-ML XML Format, Release 30 (15 MB 11/15/09)

Barley1 BLASTP annotations, CSV Format, Release 30 (5 KB 11/16/09)

Barley1 Annotations, CSV format, Release 32 (1 MB 06/09/11)

Sequence Files

Barley1 Control Sequences, FASTA (20 KB 06/24/03)

Barley1 Exemplar Sequences, FASTA (7 MB 06/24/03)

Barley1 Probe Sequences, FASTA (5 MB 08/20/08)

Barley1 Probe Sequences, Tabular (4 MB 08/20/08)

Barley1 Target Sequences, FASTA (4 MB 08/20/08)

Archived NetAffx Annotation Files

Barley1 BLASTP annotations, CSV format, Release 21 (54 KB 11/15/06)

Barley1 Annotations, MAGE-ML XML format, Release 21 (15 MB 06/15/07)

Barley1 Annotations, CSV format, Release 21 (1 MB 05/31/07)

Barley1 Annotations, MAGE-ML XML, Release 20 (15 MB 06/15/07)

Barley1 Annotations, CSV format, Release 25 (1 MB 03/18/08)

Barley1 Annotations, MAGE-ML XML Format, Release 25 (15 MB 03/18/08)

Barley1 Annotations, CSV, Release 20 (1 MB 05/31/07)

Barley1 BLASTP annotations, CSV Format, Release 25 (2 KB 03/18/08)

Barley1 Annotations, CSV format, Release 22 (1 MB 05/31/07)

Barley1 Annotations, MAGE-ML XML Format, Release 22 (15 MB 06/15/07)

Barley1 BLASTP annotations, CSV Format, Release 22 (55 KB 03/09/07)

Barley1 Annotations, CSV format, Release 23 (1 MB 07/12/07)

Barley1 Annotations, MAGE-ML XML Format, Release 23 (15 MB 07/12/07)

Barley1 BLASTP annotations, CSV Format, Release 23 (36 KB 07/12/07)

Barley1 Annotations, CSV format, Release 24 (1 MB 11/06/07)

Barley1 Annotations, MAGE-ML XML Format, Release 24 (15 MB 11/06/07)

Barley1 BLASTP annotations, CSV Format, Release 24 (3 KB 11/06/07)

Barley1 Annotations, CSV format, Release 26 (1 MB 07/08/08)

Barley1 Annotations, MAGE-ML XML Format, Release 26 (15 MB 07/08/08)

Barley1 BLASTP annotations, CSV Format, Release 26 (2 KB 07/08/08)

Barley1 Annotations, CSV format, Release 27 (1 MB 11/30/08)

Barley1 Annotations, MAGE-ML XML Format, Release 27 (15 MB 11/24/08)

Barley1 Annotations, CSV format, Release 28 (1 MB 03/12/09)

Barley1 Annotations, MAGE-ML XML Format, Release 28 (15 MB 03/12/09)

Barley1 BLASTP annotations, CSV Format, Release 28 (1 KB 03/04/09)

Barley1 Annotations, CSV format, Release 29 (1 MB 07/01/09)

Barley1 Annotations, MAGE-ML XML Format, Release 29 (15 MB 07/01/09)

Barley1 BLASTP annotations, CSV Format, Release 29 (2 KB 07/01/09)

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