Functional Genomics of Ozone Stress in Arabidopsis.
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE5722 | GEO | 2007/01/08
SECONDARY ACCESSION(S): PRJNA97019
REPOSITORIES: GEO
Similar Datasets
Project description:Ozone is known to induce gene expression in plants. The roles of the induced genes and the molecular basis for the induction however largely remain to be elucidated. We will expose 2 week-old Arabidopsis seedlings to 200 ppb ozone for 1 h. RNA will be extracted from control and ozone-fumigated seedlings 3 h following the end of the fumigation period. The induction of the known anti-oxidant enzyme GST will be confirmed prior to submission of the RNA samples to GARNet. Changes in gene expression will be assessed by hybridising microarrays with fluorescently labelled cDNA prepared from control and ozone-fumigated seedlings. The role of selected genes will be inferred from their sequence and further established by over expression under the control of the 35S or cell-specific promoters and by searching for mutants among single transposon or T-DNA insertion collections. Plants will be analysed on the basis of traits that are known to be affected by ozone including growth, flowering and stomatal responses. In addition, the ozone calcium signature we have reported previously (Clayton et al.1999) will be studied by crossing transgenic or mutant plants with apoaequorin or yellow cameleon 2.1-transformed plants. Experimenter name = Eleri Short; Experimenter phone = 01524 593929; Experimenter fax = 01524 843854; Experimenter department = Department of Biological Sciences; Experimenter institute = Lancaster University; Experimenter address = Department of Biological Sciences; Experimenter address = Lancaster University; Experimenter address = Lancaster; Experimenter zip/postal_code = LA1 4YQ; Experimenter country = UK Experiment Overall Design: 6 samples were used in this experiment
2008-06-14 | E-GEOD-5722 | biostudies-arrayexpress
Project description:AIM: 1. To identify genes that respond to N-deficiency and N-resupply and 2. To identify the subset of these genes that are under the (direct or indirect) regulatory influence of the ANR1 MADS-box gene and which may therefore participate in the nutritional regulation of root architecture. BACKGROUND: The Arabidopsis ANR1 gene is a key regulator of root architecture (Zhang and Forde, 1998): When ANR1 expression is suppressed (by antisense or co-suppression) the resulting lines are no longer able to proliferate their lateral roots in response to localised supplies of NO3- (Zhang and Forde, 1998). ANR1 encodes a root-specific member of the MADS box family of transcription factors and is thought to be a component of a signalling pathway that links an external NO3- signal to increase meristematic activity in the lateral root meristem (Zhang et al., 1999). ANR1 expression is modulated by changes in the NO3- supply (Zhang and Forde, 1998; Y.Gan and B.G. Forde, unpublished observations). In this experiment we will study the global changes in gene expression that occur when Arabidopsis plants are exposed to three different N regimes that are known to modulate ANR1 expression. The treatments will be done on wild-type plants and on an ANR1 knockout mutant as a means of identifying the (direct and indirect) downstream targets of ANR1. This experiment is complementary to another microarray experiment (BBSRC grant no. 89/P13011) which is using a DEX-inducible ANR1 transgene to identify genes that are immediately downstream of ANR1 in the signal transduction cascade Experimental: Plants of the two genotypes will be grown in hydroponic culture in a growth cabinet for 4-5 weeks before subjecting them to the different N treatments: 1) Continuous nitrate supply; 2) N deprivation for 2.5 days; and 3) N deprivation followed by 3 h nitrate induction. All harvesting will be done simultaneously to avoid diurnal effects. Roots from 12 seedlings will be harvested and pooled with roots from 12 seedlings whose treatment has been staggered by 24 h. We propose to replicate the experiment three times. References: Zhang, H. and Forde, B.G. (1998) Science 279, 407-409. Zhang, H. et al. (1999) Proc. Natl Acad. Sci. USA 96, 6529-6534. Experimenter name: Yinbo Gan Experimenter phone: 01524 592935 Experimenter fax: 01524 843854 Experimenter department: Lancaster University Experimenter address: Department of Biological Sciences Experimenter address: Lancaster University Experimenter address: Bailrigg Experimenter address: Lancaster Experimenter zip/postal_code: LA1 4YQ Experimenter country: UK Keywords: genetic_modification_design; growth_condition_design
2007-01-22 | GSE6824 | GEO
Project description:AIM:; 1. To identify genes that respond to N-deficiency and N-resupply and; 2. To identify the subset of these genes that are under the (direct or indirect) regulatory influence of the ANR1 MADS-box gene and which may therefore participate in the nutritional regulation of root architecture. BACKGROUND:; The Arabidopsis ANR1 gene is a key regulator of root architecture (Zhang and Forde, 1998): When ANR1 expression is suppressed (by antisense or co-suppression) the resulting lines are no longer able to proliferate their lateral roots in response to localised supplies of NO3- (Zhang and Forde, 1998). ANR1 encodes a root-specific member of the MADS box family of transcription factors and is thought to be a component of a signalling pathway that links an external NO3- signal to increase meristematic activity in the lateral root meristem (Zhang et al., 1999). ANR1 expression is modulated by changes in the NO3- supply (Zhang and Forde, 1998; Y.Gan and B.G. Forde, unpublished observations). In this experiment we will study the global changes in gene expression that occur when Arabidopsis plants are exposed to three different N regimes that are known to modulate ANR1 expression. The treatments will be done on wild-type plants and on an ANR1 knockout mutant as a means of identifying the (direct and indirect) downstream targets of ANR1. This experiment is complementary to another microarray experiment (BBSRC grant no. 89/P13011) which is using a DEX-inducible ANR1 transgene to identify genes that are immediately downstream of ANR1 in the signal transduction cascade; Experimental:; Plants of the two genotypes will be grown in hydroponic culture in a growth cabinet for 4-5 weeks before subjecting them to the different N treatments:; 1) Continuous nitrate supply;; 2) N deprivation for 2.5 days; and; 3) N deprivation followed by 3 h nitrate induction. All harvesting will be done simultaneously to avoid diurnal effects. Roots from 12 seedlings will be harvested and pooled with roots from 12 seedlings whose treatment has been staggered by 24 h. We propose to replicate the experiment three times. References: Zhang, H. and Forde, B.G. (1998) Science 279, 407-409. Zhang, H. et al. (1999) Proc. Natl Acad. Sci. USA 96, 6529-6534. Experimenter name: Yinbo Gan; Experimenter phone: 01524 592935; Experimenter fax: 01524 843854; Experimenter department: Lancaster University; Experimenter address: Department of Biological Sciences; Experimenter address: Lancaster University; Experimenter address: Bailrigg; Experimenter address: Lancaster; Experimenter zip/postal_code: LA1 4YQ; Experimenter country: UK Experiment Overall Design: 6 samples were used in this experiment
2008-06-15 | E-GEOD-6824 | biostudies-arrayexpress
Project description:The aim is to study the function of peroxisomal NAD-malate dehydrogenase in fatty acid beta-oxidation, glyoxylate cycle and photorespiration. Both peroxisomal MDH genes (At2g22780 and At5g09660) have been knocked out with T-DNA insertions and a double mutant made. Double mutant seedlings are blocked in beta-oxidation - they are 2,4DB resistant and beta-oxidation genes are repressed. They carry out glyoxylate cycle as normal. Plants grow well in soil and produce seed. Microarray analysis will tell us the extent of changes in gene expression in the mutant. For microarray analysis seeds are stratified at 4 C on agar medium with 1/2 strength M&S salts and 1% sucrose for 2 days, then seedlings grown for 2 days at 20 C in the light (100 umol/m2/s). Triplicate samples will be grown for mutant and wild type (col-0) and RNA isolated from each. Experimenter name = Itsara Pracharoenwattana Experimenter phone = 0131 650 5316 Experimenter fax = 0131 650 5392 Experimenter department = Institute of Molecular Plant Sciences Experimenter institute = University of Edinburgh Experimenter address = Daniel Rutherford Building University of Edinburgh Experimenter address = The King's Buildings Experimenter address = Edinburgh Experimenter zip/postal_code = EH9 3JH Experimenter country = UK Keywords: genetic_modification_design
2007-01-08 | GSE5641 | GEO
Project description:Our aim is to study the circadian expression of genes to aid in our attempt of modelling the Arabidopsis circadian clock. Circadian microarray data have previously been published for plants after white light (WL)-dark cycles, using the 8k chip (Harmer et al. 2000). We intend to repeat this experiment using the 26k chips and are coordinating with Dr. Harmer, who is pursuing complementary experiments in UC Davis. Plants will be transferred to continuous WL after entrainment to 12h:12h light dark cycles. RNAs will be harvested every 4 hours over two days, with the same accession and sampling intervals used previously by Harmer et al. The two days of sampling provide internal replication. Our experience shows that this is the most economical design: it is easier to identify rhythms over a two-day timecourse than in two replicates of a single day. Hence: 13 RNA samples on 13 chips in total. METHOD: Seed was sown on MS agar plates with 3% sucrose, imbibed at 4 C for 96 hours. Seed was then entrained for 7 days at 22C, in cycles of 12 hours white light, 12 hours darkness. After 7 days they were transferred to constant white light at 22 C: this is time 0h. Tissue harvested at the time points shown after time 0. Experimenter name = Kieron Edwards Experimenter phone = 024 7652 8374 Experimenter fax = 024 7652 3701 Experimenter department = Department of Biological Sciences Experimenter institute = University of Warwick Experimenter address = Department of Biological Sciences Experimenter address = University of Warwick Experimenter address = Gibbet Hill Road Experimenter address = Coventry Experimenter zip/postal_code = CV4 7AL Experimenter country = UK Keywords: time_series_design, growth_condition_design
2007-01-08 | GSE5612 | GEO
Project description:Trichoderma spp. are ubiquitous soil-borne ascomycetous fungi that have been used widely in the biological control of plant diseases. Certain strains also exhibit growth promotion of plants, but the mechanism for this phenomenon has not yet been elucidated. We have recently identified an isolate of T. hamatum that causes significant increases in the development of Arabidopsis root systems. The aim of this work is to elucidate the mechanism of root growth promotion. One approach is to analyse the transcriptome of plants grown in the presence and absence of the fungus. Experimenter name = Christopher Thornton Experimenter phone = 01392 264653 / 01392 264689 Experimenter department = Washington Singer Lab Experimenter address = School of Biological and Chemical Sciences Experimenter address = University of Exeter Experimenter address = Perry Road, Exeter, Experimenter zip/postal_code = EX4 4QG Experimenter country = UK Keywords: pathogenicity_design, stimulus_or_stress_design
2007-01-08 | GSE5640 | GEO
Project description:Microarray experiment was performed using 4-week old plants to compare transcriptional profiles between sni1 (suppressor of npr1) and wild type (Col-0). Three biological replicates were included. Experimenter name: Wendy Durrant Experimenter phone: 1(919)613-8175 Experimenter fax: 1(919)613-8177 Experimenter department: Durrant Lab Experimenter institute: Duke University Experimenter address: Rm. B354, LSRC Bldg. Experimenter address: Research Dr. Experimenter address: Duke University Experimenter address: Durham, NC Experimenter zip/postal_code: 27708 Experimenter country: USA Keywords: genetic_modification_design;
2007-01-22 | GSE6827 | GEO
Project description:This experiment was annotated by TAIR (http://arabidopsis.org). This experiment studies the response of gene expression in roots of 25-35 day old plants grown on hydroponics after 6, 48 and 96 hours of potassium starvation. RNA from roots was extracted after transfer to control (control) or potassium free nutrient solution respectively (starvation). Experimenter name = Julian Schroeder Experimenter phone = 619-534-7759 Experimenter fax = 619-534-7108 Experimenter department = J Schroeder Laboratory Experimenter institute = University of California-San Diego Experimenter address = Biology Department Experimenter address = University of California-San Diego Experimenter address = La Jolla Experimenter zip/postal_code = CA 92093-0116 Experimenter country = USA Keywords: time_series_design; growth_condition_design
2007-01-08 | GSE5744 | GEO
Project description:The purpose of this set of arrays is to provide a third replicate to use in data analysis addition to the 2 previous replicates for all samples already generated on this project. Our hypothesis is that adaptation to a calcareous environment will be reflected in altered gene expression including genes encoding transporters, ion channels, transcription factors, etc. To test this hypothesis we grew a laboratory non-calcicole (Col-4) and a laboratory calcicole (Cal-0) ecotypes of A. thaliana at low (1 mM) and high (12.5 mM) rhizospheric Ca2+ and compare the patterns of gene expression by microarray analysis. We then collected from the wild, a putative calcicole ecotype (Elland)and a putative non-calcicole (Penicuik) and grew both at low (1 mM) and high (12.5 mM) rhizospheric Ca2+ and compared expression profiles to the laboratory ecotypes. Experimenter name = Bev Abram Experimenter phone = 01524 592931 Experimenter address = Dept Biological Sciences Experimenter address = Lancaster University Experimenter address = Bailrigg Experimenter address = Lancaster Experimenter zip/postal_code = LA1 4YQ Experimenter country = UK Keywords: growth_condition_design; strain_or_line_design
2006-08-15 | GSE5523 | GEO
Project description:The aim is to study the function of peroxisomal NAD-malate dehydrogenase in fatty acid beta-oxidation, glyoxylate cycle and photorespiration. Both peroxisomal MDH genes (At2g22780 and At5g09660) have been knocked out with T-DNA insertions and a double mutant made. Double mutant seedlings are blocked in beta-oxidation - they are 2,4DB resistant and beta-oxidation genes are repressed. They carry out glyoxylate cycle as normal. Plants grow well in soil and produce seed. Microarray analysis will tell us the extent of changes in gene expression in the mutant. For microarray analysis seeds are stratified at 4 C on agar medium with 1/2 strength M&S salts and 1% sucrose for 2 days, then seedlings grown for 2 days at 20 C in the light (100 umol/m2/s). Triplicate samples will be grown for mutant and wild type (col-0) and RNA isolated from each. Experimenter name = Itsara Pracharoenwattana; Experimenter phone = 0131 650 5316; Experimenter fax = 0131 650 5392; Experimenter department = Institute of Molecular Plant Sciences; Experimenter institute = University of Edinburgh; Experimenter address = Daniel Rutherford Building University of Edinburgh; Experimenter address = The King's Buildings; Experimenter address = Edinburgh; Experimenter zip/postal_code = EH9 3JH; Experimenter country = UK Experiment Overall Design: 6 samples were used in this experiment
2008-06-13 | E-GEOD-5641 | biostudies-arrayexpress