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Spatial transcriptomic analysis of the Arabidopsis thaliana - Botrytis cinerea interaction

ABSTRACT: A 10 ul drop of B. cinerea spores prepared in half-strength commercial grape juice was placed in the middle of detached Arabidopsis leaves. A cock-borer of 6 mm diameter was used to harvest leaf discs starting from the edge of the lesion (close, 0-6 mm) and the edge of the first disc (away, 6-12 mm) 48 hr after inoculation. Control plants were inoculated with a 10 ul drop of half-strength commercial grape juice with no spores.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE24444 | GEO | 2011/03/01

SECONDARY ACCESSION(S): PRJNA132683

REPOSITORIES: GEO

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Spatial transcriptomic analysis of the Arabidopsis thaliana - Botrytis cinerea interaction

Project description:A 10 ul drop of B. cinerea spores prepared in half-strength commercial grape juice was placed in the middle of detached Arabidopsis leaves. A cock-borer of 6 mm diameter was used to harvest leaf discs starting from the edge of the lesion (close, 0-6 mm) and the edge of the first disc (away, 6-12 mm) 48 hr after inoculation. Control plants were inoculated with a 10 ul drop of half-strength commercial grape juice with no spores. Three Biological replicates were done of which the third replicate was a dye-swap. In total 12 samples were analyzed. Each array constituted one replicate making six arrays for the whole experiment.

2011-03-01 | E-GEOD-24444 | biostudies-arrayexpress

Transcriptomic response of Saccharomyces cerevisiae in mixed-culture wine fermentation with Hanseniaspora guilliermondii

Project description:Natural grape-juice fermentations involve the sequential development of different yeast species which strongly influence the chemical and sensorial traits of the final product. In the present study,we aimed to examine the transcriptomic response of Saccharomyces cerevisiae to the presence of Hanseniaspora guilliermondii wine fermentation. Paralell fermentations were carried out in natural grape-juice using S. cerevisiae for both single and mixed culture with a H. guilliermondii strain. For RNA extraction, cells were collected at 24h, 48h and 96 h from both fermentations

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The VELVET complex in the gray mold fungus Botrytis cinerea: impact of BcLAE1 on differentiation, secondary metabolism and virulence

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The VELVET complex in the gray mold fungus Botrytis cinerea: impact of BcLAE1 on differentiation, secondary metabolism and virulence

Project description:Full transcriptomes of the Botrytis cinerea wild-type strain B0510 and the null-mutants deltaBcVEL1 and deltaBcLAE1, cultured onto solid grape juice medium with cellophane overlays , were compared to identify BcVEL1 or/and BcLAE1-dependent genes. The Botrytis cinerea wild-type strain and the null-mutants deltaBcVEL1 and BcLAE1 were cultured for 48h onto solid grape juice medium with cellophane overlays. 4 replicates were performed. The 12 total-RNA samples (3 strains* 4 replicates) were used for hybridization on NimbleGen 4plex gene expression arrays (20,885 gene models from Botrytis cinerea with three 60-mer probes per gene).

2015-02-01 | E-GEOD-63021 | biostudies-arrayexpress

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.]

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Genome-wide fitness profiling of the homozygous and heterozygous diploid yeast deletion collection in the context of fermentation

Project description:Homozygous and heterozygous yeast deletion collections were profiled over the course of a 14 day fermentation in synthetic grape juice. Samples were compared to day 1 of the fermentation.

2011-09-30 | E-MEXP-3332 | biostudies-arrayexpress

Transcriptomic response of Saccharomyces cerevisiae in mixed-culture wine fermentation with Hanseniaspora guilliermondii

2015-12-24 | GSE66521 | 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

Transcription profiling of blood from participants with subjective memory decline

Project description:We have tested effect of bilberry/grape-juice on whole blood cell gene-expression in a nine-week double blind, placebo-controlled, dietary intervention study of aged men (n=62 - 67y) with subjective memory decline randomized to bilberry/grape- or control group (placebo). Blood-samples were collected at pre- and post intervention. Ten individuals of each group, with high baseline plasma-isoprostanes (> 86 pg/ml) were selected for blood cell gene expression profiling (Affymetrix Human-Genome U133 Plus 2.0).

2011-03-31 | E-MTAB-274 | biostudies-arrayexpress

Anti-metastatic potential of anthocyanins and their metabolites (metabotypes) on cancer cell lines with different phenotypes - role of intestinal fermentation and metabolization.

Project description:Interventions: Group 1: Arm 1 - 0.33 L Anthocyanin-rich blueberry / grape juice daily for 28 days. This is followed by a wash-out period of 10 days and a run-in phase of 7 days. Group 2: Arm 1 - 0.33 L Anthocyanin-reduced blueberry / grape juice daily for 28 days. This is followed by a wash-out period of 10 days and a run-in phase of 7 days. Primary outcome(s): Inhibition of tumor cell migration in vitro after application of plasma-isolated anthocyanins and metabolites. The endpoint is recorded after 28 days compared to day 1. Study Design: Allocation: Randomized controlled study; Masking: Blinded (masking used); Control: placebo; Assignment: crossover; Study design purpose: basic science

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