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Platform GPL1340 Query DataSets for GPL1340
Status Public on Jul 09, 2004
Title [Barley1] Affymetrix Barley Genome Array
Technology type in situ oligonucleotide
Distribution commercial
Organism Hordeum vulgare
Manufacturer Affymetrix
Manufacture protocol see manufacturer's web site
 
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
 
Web link http://www.affymetrix.com/support/technical/byproduct.affx?product=barley1
http://www.affymetrix.com/analysis/index.affx
Submission date Jul 09, 2004
Last update date Nov 21, 2011
Organization Affymetrix, Inc.
E-mail(s) [email protected], [email protected]
Phone 888-362-2447
URL http://www.affymetrix.com/index.affx
Street address
City Santa Clara
State/province CA
ZIP/Postal code 95051
Country USA
 
Samples (1802) GSM39090, GSM39091, GSM39092, GSM39093, GSM39094, GSM39095 
Series (65)
GSE2166 Wheat Freeze-Tolerance
GSE3097 Barley1 salinity stress study
GSE3170 Barley single feature polymorphisms and drought stress gene expression

Data table header descriptions
ID Affymetrix Probe Set ID
GB_ACC GenBank Accession Number
CLONE_ID link in Entrez Nucleotides database
SPOT_ID Column added by GEO staff to facilitate sequence tracking in Entrez GEO
Species Scientific Name
Annotation Date The date that the annotations for this probe array were last updated. It will generally be earlier than the date when the annotations were posted on the Affymetrix web site.
Sequence Type Indicates whether the sequence is an Exemplar, Consensus or Control sequence. An Exemplar is a single nucleotide sequence taken directly from a public database. This sequence could be an mRNA or EST. A Consensus sequence, is a nucleotide sequence assembled by Affymetrix, based on one or more sequence taken from a public database.
Representative Public ID The accession number of a representative sequence. Note that for consensus-based probe sets, the representative sequence is only one of several sequences (sequence sub-clusters) used to build the consensus sequence and it is not directly used to derive the probe sequences. The representative sequence is chosen during array design as a sequence that is best associated with the transcribed region being interrogated by the probe set. Refer to the "Sequence Source" field to determine the database used.
Sequence Source
Target Description GenBank description associated with the representative public identifier. Blank for some probe sets.
Gene Title
Gene Symbol
ENTREZ_GENE_ID Entrez Gene Database UID
Gene Ontology Biological Process Gene Ontology Consortium Biological Process derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".
Gene Ontology Cellular Component Gene Ontology Consortium Cellular Component derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".
Gene Ontology Molecular Function Gene Ontology Consortium Molecular Function derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".

Data table
ID GB_ACC CLONE_ID SPOT_ID Species Scientific Name Annotation Date Sequence Type Representative Public ID Sequence Source Target Description Gene Title Gene Symbol ENTREZ_GENE_ID Gene Ontology Biological Process Gene Ontology Cellular Component Gene Ontology Molecular Function
1200459_Reg_88-1740_at 1200459_Reg_88-1740 Hordeum vulgare Mar 11, 2009 Exemplar sequence 1200459_Reg_88-1740 Affymetrix Proprietary Database From cloning vector pGL3-Basic, firefly luciferase (luc) gene
1289374_Reg_826-1545_at 1289374_Reg_826-1545 Hordeum vulgare Mar 11, 2009 Exemplar sequence 1289374_Reg_826-1545 Affymetrix Proprietary Database Cloning vector phGFP-S65T, complete sequence, green fluorescent protein (gfp) gene, complete cds
149174_Reg_66-1115_at 149174_Reg_66-1115 Hordeum vulgare Mar 11, 2009 Exemplar sequence 149174_Reg_66-1115 Affymetrix Proprietary Database K. pneumoniae bromoxynil-specific nitrilase (bxn) gene, complete cds
150775_Reg_211-1236_at 150775_Reg_211-1236 Hordeum vulgare Mar 11, 2009 Exemplar sequence 150775_Reg_211-1236 Affymetrix Proprietary Database Plasmid pJR225 (from E.coli) hygromycin B phosphotransferase (hgh) gene, complete cds
23381122_R_1101-1898_at 23381122_R_1101-1898 Hordeum vulgare Mar 11, 2009 Exemplar sequence 23381122_R_1101-1898 Affymetrix Proprietary Database From binary vector pGV4042, region between right and left T-DNA border and neomycin phosphotransferase (nptII) gene
2623978_R_1403-2212_at 2623978_R_1403-2212 Hordeum vulgare Mar 11, 2009 Exemplar sequence 2623978_R_1403-2212 Affymetrix Proprietary Database Synthetic DNA containing kanamycin and geneticin (G418) resistance gene in Escherichia coli plasmid pFA6a-GFPS65T-kanMX6
40321-46140.AF427791_x_at --Control Hordeum vulgare Mar 11, 2009 Control sequence 40321-46140.AF427791 Affymetrix Proprietary Database Intergenic region between Morex BAC predicted Stowaway.3 and BARE-1 SoloLTR-1.2; intergenic region, flanking CDS (711N16.9 and 711N16.8) are methylated in 7-day old leaves, but are expressed via rtPCR assay.
48446_Reg_1231-2205_at 48446_Reg_1231-2205 Hordeum vulgare Mar 11, 2009 Exemplar sequence 48446_Reg_1231-2205 Affymetrix Proprietary Database V.harveyi luxA and luxB genes for luciferase alpha and beta subunits, luxB gene
48446_Reg_137-1204_at 48446_Reg_137-1204 Hordeum vulgare Mar 11, 2009 Exemplar sequence 48446_Reg_137-1204 Affymetrix Proprietary Database From V. harveyi luxA and luxB genes for luciferase alpha and beta subunits, luxA gene
74797-75570.AF427791_x_at --Control Hordeum vulgare Mar 11, 2009 Control sequence 74797-75570.AF427791 Affymetrix Proprietary Database Intergenic region between Morex BAC predicted CDS 80H14.15 and 80H14.14; both 80H14.15 and 80H14.14 CDS are not expressed in 7-day old leaves via rtPCR assay
8829-9073.AF427791_x_at --Control Hordeum vulgare Mar 11, 2009 Control sequence 8829-9073.AF427791 Affymetrix Proprietary Database Intergenic region between Morex BAC predicted tRNA ser and CDS 711N16.14; 711N16.14 CDS is not expressed in 7-day old leaves via rtPCR assay.
9507414_R_4264-4644_at 9507414_R_4264-4644 Hordeum vulgare Mar 11, 2009 Exemplar sequence 9507414_R_4264-4644 Affymetrix Proprietary Database From complete sequence of plasmid pRL1063a, bleomycin resistance gene
A00196.1_at A00196.1 Hordeum vulgare Mar 11, 2009 Exemplar sequence A00196.1 Affymetrix Proprietary Database A00196 Synthetic uidA gene for beta-glucuronidase (GUS)
A06498.1_s_at A06498.1 Hordeum vulgare Mar 11, 2009 Exemplar sequence A06498.1 Affymetrix Proprietary Database Artificial sequence for nopaline synthase
AB011264_at AB011264 Hordeum vulgare Mar 11, 2009 Exemplar sequence AB011264 Affymetrix Proprietary Database BEST BLASTX NR: 11/06/02 BAA74581.1 0.0 (AB011264) nicochianamine synthase 3 [Hordeum vulgare subsp. vulgare] 0030418 // nicotianamine biosynthetic process // inferred from electronic annotation 0016740 // transferase activity // inferred from electronic annotation /// 0030410 // nicotianamine synthase activity // inferred from electronic annotation
AB011266_at AB011266 Hordeum vulgare Mar 11, 2009 Exemplar sequence AB011266 Affymetrix Proprietary Database BEST BLASTX NR: 11/06/02 BAA74583.1 0.0 (AB011266) nicotianamine Synthase 4 [Hordeum vulgare subsp. vulgare] 0030418 // nicotianamine biosynthetic process // inferred from electronic annotation 0016740 // transferase activity // inferred from electronic annotation /// 0030410 // nicotianamine synthase activity // inferred from electronic annotation
AB019525_at AB019525 Hordeum vulgare Mar 11, 2009 Exemplar sequence AB019525 Affymetrix Proprietary Database BEST BLASTX NR: 11/06/02 BAA74587.1 0.0 (AB019525) nicotianamine synthase 7 [Hordeum vulgare subsp. vulgare] 0030418 // nicotianamine biosynthetic process // inferred from electronic annotation 0016740 // transferase activity // inferred from electronic annotation /// 0030410 // nicotianamine synthase activity // inferred from electronic annotation
AB024007_at AB024007 Hordeum vulgare Mar 11, 2009 Exemplar sequence AB024007 Affymetrix Proprietary Database BEST BLASTX NR: 11/06/02 BAB07798.1 e-104 (AB024007) IDS3 [Hordeum vulgare subsp. vulgare] 0016491 // oxidoreductase activity // inferred from electronic annotation
AF016328_at AF016328 Hordeum vulgare Mar 11, 2009 Exemplar sequence AF016328 Affymetrix Proprietary Database BEST BLASTX NR: 11/06/02 AAB02259.1 2e-67 permatin precursor
AF026538_at AF026538 Hordeum vulgare Mar 11, 2009 Exemplar sequence AF026538 Affymetrix Proprietary Database BEST BLASTX NR: 11/06/02 A59232 e-161 ABA-responsive protein - barley gb|AAD09343.1| (AF026538) ABA-responsive protein [Hordeum vulgare] ABA-responsive protein LOC548112 548112

Total number of rows: 22840

Table truncated, full table size 5423 Kbytes.






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