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Cross-species Detection in Barley1 GeneChip Array

ABSTRACT: This study was conducted to evaluate the efficiency of cross-species detection in Barley1 GeneChip array. We hybridized cRNA derived from first leaves of barley green seedlings (as a control), as well as the same stage of seedling leaf from representative genotypes of wheat, oat, rice, maize, and sorghum. Ten to twenty seedlings for each species were harvested and pooled for RNA preparation, labeling, and hybridization. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rico Caldo. The equivalent experiment is BB1 at PLEXdb.]

ORGANISM(S): Oryza sativa Avena sativa Zea mays Triticum aestivum Hordeum vulgare Sorghum bicolor

PROVIDER: GSE33391 | GEO | 2011/11/22

SECONDARY ACCESSION(S): PRJNA149123

REPOSITORIES: GEO

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Cross-species Detection in Barley1 GeneChip Array

Project description:This study was conducted to evaluate the efficiency of cross-species detection in Barley1 GeneChip array. We hybridized cRNA derived from first leaves of barley green seedlings (as a control), as well as the same stage of seedling leaf from representative genotypes of wheat, oat, rice, maize, and sorghum. Ten to twenty seedlings for each species were harvested and pooled for RNA preparation, labeling, and hybridization. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rico Caldo. The equivalent experiment is BB1 at PLEXdb.] species: Barley(2-replications); species: Wheat(2-replications); species: Oat(2-replications); species: Sorghum(2-replications); species: Corn(2-replications); species: Rice(2-replications)

2011-11-22 | E-GEOD-33391 | biostudies-arrayexpress

Mla-specified Transcriptional Responses in Barley-Powdery Mildew Interactions

Project description:A large-scale parallel expression analysis was conducted to elucidate Mla-specified responses to powdery mildew infection using 22K Barley1 GeneChip probe arrays. Our goal was to identify genes differentially expressed in incompatible (resistant) vs. compatible (susceptible) and Mla-specified Rar1-dependent vs. -independent interactions. A split-split-plot design with 108 experimental units (3 replications x 2 isolates x 3 genotypes x 6 time points) was used to profile near-isogenic lines containing the Mla1, Mla6, and Mla13 resistance specificities in response to inoculation with the Blumeria graminis f. sp. hordei (Bgh) isolates 5874 (AvrMla1, AvrMla6) and K1 (AvrMla1, AvrMla13). ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rico Caldo. The equivalent experiment is BB4 at PLEXdb.]

2011-11-22 | GSE33396 | GEO

Transcription profiling of barley plants containing variants of Mla1 and Mla6 powdery mildew resistance genes

Project description:A split-split-plot design with 144 experimental units (3 replications x 4 genotypes x 6 time points x 2 treatment types) was used to profile barley plants containing variants of Mla1 and Mla6 powdery mildew resistance genes in response to inoculation with the Blumeria graminis f. sp. hordei (Bgh) isolates 5874 (AvrMla1, AvrMla6). Barley leaves were harvested from inoculated and non-inoculated plants at 6 time points (0,8,16,20,24 and 32 hrs) after Bgh inoculation. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rico Caldo. The equivalent experiment is BB10 at PLEXdb.]

2011-11-22 | GSE33392 | GEO

Functional Genomic Analysis Of Barley(Hordeum vulgare L.) Grain Protein Accumulation

Project description:Effect of high grain protein locus on barley grain protein accumulation. Gene expression levels were analysed in Karl, a low grain protein variety with its near-isogenic line 10_11(has high grain protein locus, chromosome 6)using Barley1 22k affymetrix chip. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Aravind Jukanti. The equivalent experiment is BB53 at PLEXdb.]

2011-11-22 | GSE33413 | GEO

Mapping barley genes to chromosome arms by transcript profiling of wheat-barley ditelosomic chromosome addition lines

Project description:We utilized the Barley1 Affymetrix GeneChip for comparative transcript analysis of Betzes barley, Chinese Spring wheat, and Chinese Spring–Betzes ditelosomic chromosome addition lines to physically map barley genes to their respective chromosome arm locations. We mapped barley genes to chromosome arms (1HS, 2HS, 2HL, 3HS, 3HL, 4HS, 4HL, 5HS, 5HL, 7HS, and 7HL) based on their transcript levels in the ditelosomic addition lines. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Hatice Bilgic. The equivalent experiment is BB55 at PLEXdb.]

2011-11-22 | GSE33400 | GEO

Cross-species Detection in Barley1 GeneChip Array

Project description:Cross-species Detection in Barley1 GeneChip Array

| PRJNA149123 | ENA

Late response to boron toxicity in barley leaves

Project description:Barley1 GeneChip was used to investigate transcriptome changes associated with boron (B) toxicity in a sensitive barley cultivar (Hordeum vulgare L. cv. Hamidiye). Eight day old aseptically grown seedlings were subjected to 5 or 10 mM boric acid (B(OH)3) treatments for 5 days and expression profiles were determined with DNA microarrays using total RNA from leaf tissues. Surface sterilized seeds were aseptically germinated and grown on half strength Hoagland’s solution (Hoagland and Arnon, 1950) (pH 5.8) solidified with Phytagel® for 8 days at 23±2ºC with 16 h light (400 µmol m–2 s–1) and 8 h dark photo-cycle with 70% relative humidity. Seedlings were transferred to sterile hydroponic cultures for B treatment, which was applied immediately after transfer as half strength Hoagland’s solution containing either 5 mM B(OH)3 (5B) or 10 mM B(OH)3 (10B) for another 5 days under the same physical conditions. Control (C) groups were transferred to half strength Hoagland’s solution without extra B(OH)3. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Mehmet Tufan OZ. The equivalent experiment is BB63 at PLEXdb.]

2009-01-24 | GSE14521 | GEO

Comparison of isogenic lines differing in vernalization requirement

Project description:Gene expression was assyed in seedlings of isogenic barley lines differing in vernalization requirement. Seedlings were harvested after 5 days germination in darkness at 20 degrees. Seedlings were then subjected to 1 day at 4 degrees after 5 days germination in darkness at 20. Genotypes include the winter barley parent Dairokakku, and isogenic lines carrying a deletion of VRN2, active VRN1 allleles (VRN1-10, or VRN1-8) or an active allele of FT1/VRN3. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Ben Trevaskis. The equivalent experiment is BB97 at PLEXdb.]

2016-01-23 | GSE43704 | GEO

Transcription patterns during wheat development

Project description:The analysis of gene expression during wheat development: Gene expression measurements were carried out on a developmental tissue series for wild-type wheat (cv. Chinese Spring) using the Affymetrix Wheat GeneChip. Thirteen tissues at defined developmental stages were chosen to match the barley (cv. Morex) tissue series of Druka et al. 2006 that used the Affymetrix Barley1 GeneChip. Three replicates of: root tissue at two different developmental stages, leaf, crown, caryopsis, anther, pistil, inflorescence, bracts, mesocotyl, endosperm, embryo and coleoptiles were hybridised. Comparisons between this wheat data and the barley dataset were performed and are available at http://contigcomp.acpfg.com.au [PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Tim Sutton. The equivalent experiment is TA3 at PLEXdb.]

2009-08-11 | GSE12508 | GEO

Transcription profiling of barley leaves after boron reveals a late response to boron toxicity

Project description:Barley1 GeneChip was used to investigate transcriptome changes associated with boron (B) toxicity in a sensitive barley cultivar (Hordeum vulgare L. cv. Hamidiye). Eight day old aseptically grown seedlings were subjected to 5 or 10 mM boric acid (B(OH)3) treatments for 5 days and expression profiles were determined with DNA microarrays using total RNA from leaf tissues. Surface sterilized seeds were aseptically germinated and grown on half strength Hoaglandâs solution (Hoagland and Arnon, 1950) (pH 5.8) solidified with PhytagelÂ® for 8 days at 23Â±2ÂºC with 16 h light (400 Âµmol mâ2 sâ1) and 8 h dark photo-cycle with 70% relative humidity. Seedlings were transferred to sterile hydroponic cultures for B treatment, which was applied immediately after transfer as half strength Hoaglandâs solution containing either 5 mM B(OH)3 (5B) or 10 mM B(OH)3 (10B) for another 5 days under the same physical conditions. Control (C) groups were transferred to half strength Hoaglandâs solution without extra B(OH)3. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Mehmet Tufan OZ. The equivalent experiment is BB63 at PLEXdb.] Experiment Overall Design: treated or untreated: Control (C)(3-replications); treated or untreated: 5 mM B(OH)3 treatment (5B)(3-replications); treated or untreated: 10 mM B(OH)3 treatment (10B)(3-replications)

2009-01-31 | E-GEOD-14521 | biostudies-arrayexpress

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