Low chronic exposure of Arabidopsis thaliana to Caesium-137
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE5522 | GEO | 2006/08/15
SECONDARY ACCESSION(S): PRJNA96177
REPOSITORIES: GEO
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Project description:Arabidopsis thaliana plants are grown for one week in a hydroponic growth system and transferred to new plant medium containing low levels of Caesium-137 (control is transferred to new medium with no radioactivity) and left for further two weeks. Levels of Caesium-137 are chosen according to research and are reflecting occurring levels found in radioactive contaminated soil. The plants are then harvested and the samples divided into shoot and root samples. Experimenter name = Yu-Jin Heinekamp; Experimenter phone = 0044-117-3442102; Experimenter address = University of the West of England (UWE); Experimenter address = Faculty of Applied Sciences; Experimenter address = Center for Research in Plants, GRI; Experimenter address = Coldharbour Lane; Experimenter address = Bristol; Experimenter zip/postal_code = BS6 5BP; Experimenter country = UK Experiment Overall Design: 12 samples were used in this experiment
2008-06-13 | E-GEOD-5522 | biostudies-arrayexpress
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
Project description:This experiment was annotated by TAIR (http://arabidopsis.org). Col-0 suspension cells provided by Dr. C. Koncz and Dr. M. Umeda. 15 ml of Arabidopsis Col-0 suspension cells (Mathur et al. 1998) was transferred to 35 ml of a fresh modified Murashige and Skoog (MS) medium supplemented with 1 ug /ml 2,4-dichlorphenoxyacetic acid and 3% sucrose every 7 day, and cultured on a rotary shaker at 120 rpm in the dark at 22 C for subculture. For xylem vessel element induction, a 7.5 ml aliquot of 7-day-old subcultured cells was transferred into 42.5 ml of fresh medium that included 1 uM brassinolide and 10 mM H3BO3, and cultured as described above. The frequency of xylem vessel element formation was calculated as the proportion of xylem vessel elements to the number of living cells and the vessel elements. Experimenter name = Hiroo Fukuda Experimenter phone = +81-3-5841-4463 Experimenter fax = +81-3-5841-4462 Experimenter department = H Fukuda Laboratory Experimenter institute = University of Tokyo Experimenter address = Department of Biological Science Experimenter address = 2nd Buil. Experimenter address = Hongo 7-3-1, Bunkyo-ku Experimenter zip/postal_code = Tokyo 113-0033 Experimenter country = Tokyo Keywords: compound_treatment_design; time_series_design;
2007-01-08 | GSE5748 | GEO
Project description:The aim of this study is to study gene expression in Brassica oleracea in shoot tissues of plants grown under contrasting P supplies (see Hammond JP et al., 2003, Plant Physiology, 132, 578-596 for background). Seeds of B. oleracea (var. alboglabra, A12dH) were first washed in 70% (v/v) ethanol/water, rinsed in distilled water and surface sterilised using 50% (v/v) domestic bleach/water. Seeds were rinsed and imbibed for 3 to 5 days in sterile distilled water at 4°C to break dormancy. Following imbibition, B. oleracea seeds were sown in un-vented, polycarbonate culture boxes (Sigma-Aldrich Company Ltd., Dorset UK). Seedlings were grown for 21 days on perforated polycarbonate discs (diameter 91 mm by 5 mm) placed on 75 ml of 0.8% (w/v) agar containing 1% (w/v) sucrose and a basal salt mix. Roots grew into the agar, but shoots remained on the opposite side of the disc. After 21 days, seedlings were transferred, still on polycarbonate discs, to a hydroponics system situated in a Saxcil growth cabinet (16 h daylength, set to 22°C and 80% humidity). Each polycarbonate disc was placed on a light-proof 500 ml beaker over 450 ml of nutrient solution. After 7 days, half the plants were transferred to nutrient solution containing no phosphate and the other half remained on full nutrient solution (control plants). Shoots were harvested 100 h after the withdrawal of P. !Samples were snap frozen in liquid nitrogen. RNA was extracted using the TRIzol extraction method and cleaned through a Qiagen RNeasy column. Experimenter name = Martin Broadley Experimenter phone = 0115 951 6382 Experimenter fax = 0115 951 6334 Experimenter institute = University of Nottingham Experimenter address = Plant Sciences Division Experimenter address = School of Biosciences Experimenter address = University of Nottingham Experimenter address = Sutton Bonington Experimenter address = Loughborough Experimenter zip/postal_code = LE12 5RD Experimenter country = UK Keywords: growth_condition_design
2007-01-08 | GSE5614 | GEO
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 Experiment Overall Design: 18 samples were used in this experiment
2008-06-15 | E-GEOD-6825 | biostudies-arrayexpress
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:This experiment was annotated by TAIR (http://arabidopsis.org). Col-0 suspension cells provided by Dr. C. Koncz and Dr. M. Umeda. 15 ml of Arabidopsis Col-0 suspension cells (Mathur et al. 1998) was transferred to 35 ml of a fresh modified Murashige and Skoog (MS) medium supplemented with 1 ug /ml 2,4-dichlorphenoxyacetic acid and 3% sucrose every 7 day, and cultured on a rotary shaker at 120 rpm in the dark at 22 C for subculture. For xylem vessel element induction, a 7.5 ml aliquot of 7-day-old subcultured cells was transferred into 42.5 ml of fresh medium that included 1 uM brassinolide and 10 mM H3BO3, and cultured as described above. The frequency of xylem vessel element formation was calculated as the proportion of xylem vessel elements to the number of living cells and the vessel elements. Experimenter name = Hiroo Fukuda; Experimenter phone = +81-3-5841-4463; Experimenter fax = +81-3-5841-4462; Experimenter department = H Fukuda Laboratory; Experimenter institute = University of Tokyo; Experimenter address = Department of Biological Science; Experimenter address = 2nd Buil. Experimenter address = Hongo 7-3-1, Bunkyo-ku; Experimenter zip/postal_code = Tokyo 113-0033; Experimenter country = Tokyo Experiment Overall Design: 12 samples were used in this experiment
2008-06-14 | E-GEOD-5748 | biostudies-arrayexpress
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: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 Experiment Overall Design: 13 samples were used in this experiment
2008-06-13 | E-GEOD-5612 | biostudies-arrayexpress
Project description:The aim of this study is to study gene expression in Brassica oleracea in shoot tissues of plants grown under contrasting P supplies (see Hammond JP et al., 2003, Plant Physiology, 132, 578-596 for background). Seeds of B. oleracea (var. alboglabra, A12dH) were first washed in 70% (v/v) ethanol/water, rinsed in distilled water and surface sterilised using 50% (v/v) domestic bleach/water. Seeds were rinsed and imbibed for 3 to 5 days in sterile distilled water at 4°C to break dormancy. Following imbibition, B. oleracea seeds were sown in un-vented, polycarbonate culture boxes (Sigma-Aldrich Company Ltd., Dorset UK). Seedlings were grown for 21 days on perforated polycarbonate discs (diameter 91 mm by 5 mm) placed on 75 ml of 0.8% (w/v) agar containing 1% (w/v) sucrose and a basal salt mix. Roots grew into the agar, but shoots remained on the opposite side of the disc. After 21 days, seedlings were transferred, still on polycarbonate discs, to a hydroponics system situated in a Saxcil growth cabinet (16 h daylength, set to 22°C and 80% humidity). Each polycarbonate disc was placed on a light-proof 500 ml beaker over 450 ml of nutrient solution. After 7 days, half the plants were transferred to nutrient solution containing no phosphate and the other half remained on full nutrient solution (control plants). Shoots were harvested 100 h after the withdrawal of P. !Samples were snap frozen in liquid nitrogen. RNA was extracted using the TRIzol extraction method and cleaned through a Qiagen RNeasy column. Experimenter name = Martin Broadley; Experimenter phone = 0115 951 6382; Experimenter fax = 0115 951 6334; Experimenter institute = University of Nottingham; Experimenter address = Plant Sciences Division; Experimenter address = School of Biosciences; Experimenter address = University of Nottingham; Experimenter address = Sutton Bonington; Experimenter address = Loughborough; Experimenter zip/postal_code = LE12 5RD; Experimenter country = UK Experiment Overall Design: 6 samples were used in this experiment
2008-06-13 | E-GEOD-5614 | biostudies-arrayexpress