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Molecular responses to external pH changes in roots of Arabidopsis thaliana

ABSTRACT: Plants live in soils that vary considerably, both spatially and over time, in terms of nutrient composition and pH. Consistently, plants have to recognize and adapt to these changes by altering their structure and metabolism. The goal of this array analysis is to characterize the global transcriptional response to external pH changes in roots, which to date is almost unexplored. Arabidopsis thaliana (Columbia-0) were grown in hydroponic cultures in basic nutrient solution. Two days before treatment the media was shifted to nutrient solution containing 5mM MES, pH 6. At the time of the treatment start (4 hours after light on) the plants were shifted to nutrient solutions of pH 4.5 and 6.0 (control). Root RNA samples from time point 1 and 8 hour after treatment start is used for array analyzes. Keywords: Expression profilling by array

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE18982 | GEO | 2009/11/18

SECONDARY ACCESSION(S): PRJNA120973

REPOSITORIES: GEO

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Molecular responses to external pH changes in roots of Arabidopsis thaliana

Project description:Plants live in soils that vary considerably, both spatially and over time, in terms of nutrient composition and pH. Consistently, plants have to recognize and adapt to these changes by altering their structure and metabolism. The goal of this array analysis is to characterize the global transcriptional response to external pH changes in roots, which to date is almost unexplored. Arabidopsis thaliana (Columbia-0) were grown in hydroponic cultures in basic nutrient solution. Two days before treatment the media was shifted to nutrient solution containing 5mM MES, pH 6. At the time of the treatment start (4 hours after light on) the plants were shifted to nutrient solutions of pH 4.5 and 6.0 (control). Root RNA samples from time point 1 and 8 hour after treatment start is used for array analyzes. Keywords: Expression profilling by array 12 samples were used in this experiment

2009-11-17 | E-GEOD-18982 | biostudies-arrayexpress

Sugarcane transcriptome - Phosphate starvation

Project description:Rooted sugarcane plantlets, originated from in vitro meristem culture (genotype SP80-3280, CTC, Brazil), were greenhouse acclimatized by initial cultivation on 1/20th strength Hoagland and Arnon (1950) nutrient solution. Nutrient solutions were aired from an oil-less compressor and replaced every 7 days, increasing nutrient concentration to ¼ strength in 3 weeks. Plants were then individually transferred to 2.8 L pots filled with fresh ¼ strength nutrient solution. After one week, half of the plants were transferred to fresh solution containing 250 µM Pi, while the other half was transferred to nutrient solution deprived of phosphate (Pi), with H2PO4 being replaced by H2SO4 (Muchhal et al., 1996). Roots from six plants from each treatment (0 and 250 µM Pi) were harvested 6, 12, 24 and 48 h after exposure to phosphate starvation and immediately frozen in liquid nitrogen. For each time point and each treatment, root samples were aggregated in three pools of two samples each. Extraction of total RNA was performed separately on each sample pool. Keywords: time course of stress response

2007-05-20 | GSE4966 | GEO

adventitious root development P. contorta

Project description:After four weeks the primary roots were cut off from the seedlings. The hypocotyl cuttings were treated in Hoagland nutrient solution at pH 5.8 containing 1.23 mM indole-3-butyric acid(IBA) for six hours then transferred to Hoagland nutrient solution lacking IBA. The hypocotyls were harvested at the following time points: day o,3,6,9,12 and 33. Keywords: time-course

2004-04-01 | GSE1261 | GEO

Global Transcript Profiles of Maize Seedling Roots in the Presence and Absence of Nitrate

Project description:The following study was conducted to better understand the genetic response of maize roots to nitrate availability. To do so, an array was designed and created by the Plant Sciences Institute at Iowa State University. This custom array contained 7,888 informative spots of cDNA obtained from NSF Plant Genome EST projects led by Ginny Walbot and Pat Schnable. RNA was collected from root tissue at two time points: 30 minutes and 24 hours. At each time point, transcript profiles were compared between root tissues treated with 5mM calcium nitrate and controls treated with 5mM calcium sulfate. Keywords: Nutrient response in maize roots

2014-12-30 | GSE15167 | GEO

Differential gene expression patterns in potassium-starved and caesium-treated plants

2007-01-08 | GSE6160 | GEO

Differential gene expression patterns in potassium-starved and Caesium-treated plants

Project description:At high concentrations ceasium (Cs) is toxic to plant growth. This toxic effect may occur when Cs blocks potassium (K) uptake mechanisms in plants. Consequently, plants starved of K and plants exposed to toxic concentrations of Cs should have similar gene expression patterns. To test this hypothesis, Arabidopsis will initially be grown on agar containing 1/10 MS salts before being transferred to either 1/10 MS nutrient solution (control plants), 1/10 MS nutrient solution containing 2 mM Cs, or 1/10 MS nutrient solution with no K. Roots and shoot will then be harvested seven days after transfer and used to challenge ATH1 GeneChips. Experimenter name: John Hammond Experimenter phone: 01789 470382 Experimenter fax: 01789 470552 Experimenter institute: Warwick University Experimenter address: Horticulture Research International Experimenter address: Wellesbourne Experimenter address: Warwick Experimenter zip/postal_code: CV35 9EF Experimenter country: UK Keywords: compound_treatment_design

2007-01-22 | GSE6825 | GEO

Root and shoot Jamonic Acid induction in Brassica oleraceae

Project description:Brassica oleraceae plants were treated with jasmonic acid either at the roots or two leaves. An acidic (HCl) water sollution with the same pH as the jasmonic acid sollution was also applied to two leaves of the root jasmonic acid treated plants, and to the roots of leaf jasmonic acid treated plants. Control plants received a mock treatment on roots and leaves with acidic water of the same pH as the jasmonic acid sollution. The whole root system and two systemic leaves were harvested separately at 6, 18 and 30 h after treatment. For each time point, tissue and treatment, three biological replicates (except two replicates for 'Root-Cont-18h' sample) were made consisting of pooled tissue samples from 10 plants. Gene expression was analyzed in both tissues using the 29,000 element Arabidopsis Oligonucleotide Microarrays (Qiagen-Operon Arabidopsis Genome Array Ready Oligo Set version 3.0).

2012-12-18 | GSE38784 | GEO

Global proteomic analysis for stress response of Mycobacterium tuberculosis

Project description:To expand an insight into the stress adaptation in Mycobacterium tuberculosis H37Rv (Mtb), we approached the iTRAQ analysis to understand the global proteome profile of stressed Mtb under Acid (5.5 pH), Diamide (5mM) and Hydrogen peroxide (H2O2) (5mM) conditions and compared with gene expression of Mtb incubated in 7H9 rich medium (pH 7.0). The experiment was performed for overnight treatment of aforementioned stress. Whole cell lysate (WCL) from three independent repeats of control and stressed samples were labelled with three set of 4-plex iTRAQ labelling reagents (AB SCIEX) in proportion to manufacturer’s protocol.

2022-10-13 | PXD015167 | Pride

Transcription profiling of Arabidopsis potassium-starved and caesium-treated plants

2009-09-03 | E-NASC-61 | biostudies-arrayexpress

Transcription profiling of Arabidopsis potassium-starved and caesium-treated plants

Project description:At high concentrations caesium (Cs) is toxic to plant growth. This toxic effect may occur when Cs blocks potassium (K) uptake mechanisms in plants. Consequently, plants starved of K and plants exposed to toxic concentrations of Cs should have similar gene expression patterns. To test this hypothesis, Arabidopsis will initially be grown on agar containing 1/10 MS salts before being transferred to either 1/10 MS nutrient solution (control plants), 1/10 MS nutrient solution containing 2 mM Cs, or 1/10 MS nutrient solution with no K. Roots and shoot will then be harvested seven days after transfer and used to challenge ATH1 GeneChips. Experiment Overall Design: Number of plants pooled:40-50

2008-06-14 | E-GEOD-6160 | biostudies-arrayexpress

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