Transcription profiling of Arabidopsis sni1 and wild type
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Nottingham Arabidopsis Stock Centre (NASC)
PROVIDER: E-GEOD-6827 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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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;
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Project description:This data was annotated by TAIR (http://arabidopsis.org). Two week-old Arabidopsis aerial tissues from Columbia-0 and cpr5, cpr5npr1, cpr5scv1, cpr5npr1svi1, and npr1 lines were collected for analysis. Experimenter name = Jinyoung Yang Experimenter phone = 919-613-8176, 919-61 Experimenter fax = 919-613-8177 Experimenter department = DCMB GROUP Experimenter institute = Duke University Experimenter address = B361 LSRC Bldg. Experimenter address = Research Dr. Experimenter address = Durham Experimenter zip/postal_code = NC 27708 Experimenter country = USA Keywords: genetic_modification_design
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Project description:This data was annotated by TAIR (http://arabidopsis.org). Two week-old Arabidopsis aerial tissues from Columbia-0 and cpr5, cpr5npr1, cpr5scv1, cpr5npr1svi1, and npr1 lines were collected for analysis. Experimenter name = Jinyoung Yang; Experimenter phone = 919-613-8176, 919-61; Experimenter fax = 919-613-8177; Experimenter department = DCMB GROUP; Experimenter institute = Duke University; Experimenter address = B361 LSRC Bldg. Experimenter address = Research Dr. Experimenter address = Durham; Experimenter zip/postal_code = NC 27708; Experimenter country = USA Experiment Overall Design: 12 samples were used in this experiment
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Project description:This experiment was donated by Philip N. Benfey's lab through ArexDB (http://www.arexdb.org). A global map of gene expression within an organ can identify genes with coordinated expression in localized domains, thereby relating gene activity to cell fate and tissue specialization. Here, we present localization of expression of more than 22,000 genes in the Arabidopsis root. Gene expression was mapped to 15 different zones of the root that correspond to cell types and tissues at progressive developmental stages. Patterns of gene expression traverse traditional anatomical boundaries and show cassettes of hormonal response. Chromosomal clustering defined some coregulated genes. This expression map correlates groups of genes to specific cell fates and should serve to guide reverse genetics. Experimenter name = Kenneth Birnbaum Experimenter department = Benfey Lab Experimenter institute = Duke University Experimenter address = Department of Biology Experimenter address = Duke University Experimenter address = Box 91000 Experimenter address = Durham Experimenter zip/postal_code = NC 27708 Experimenter country = America Keywords: cell_type_comparison_design
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Project description:This experiment was donated by Philip N. Benfey's lab through ArexDB (http://www.arexdb.org). A global map of gene expression within an organ can identify genes with coordinated expression in localized domains, thereby relating gene activity to cell fate and tissue specialization. Here, we present localization of expression of more than 22,000 genes in the Arabidopsis root. Gene expression was mapped to 15 different zones of the root that correspond to cell types and tissues at progressive developmental stages. Patterns of gene expression traverse traditional anatomical boundaries and show cassettes of hormonal response. Chromosomal clustering defined some coregulated genes. This expression map correlates groups of genes to specific cell fates and should serve to guide reverse genetics. Experimenter name = Kenneth Birnbaum; Experimenter department = Benfey Lab; Experimenter institute = Duke University; Experimenter address = Department of Biology; Experimenter address = Duke University; Experimenter address = Box 91000; Experimenter address = Durham; Experimenter zip/postal_code = NC 27708; Experimenter country = America Experiment Overall Design: 27 samples were used in this experiment
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Project description:The aim of this BBSRC-funded project is to develop laser-capture microdissection (LCMD) to isolate small cell clusters in different regions of arabidopsis embryos at different stages of development; to develop RNA amplification procedures on dissected tissue sampes; and to use DNA microarray techniques to investigate global transcriptional differences between samples. Cryosectioned embryos of ecotype Col-O of globular, heart and torpedo stage were used to isolate cell clusters from the apical and basal regions, for RNA isolation and amplification. !Samples will be provided as T7-primed cDNA, with three biological replicates for each tissue to be analysed. Each replicate comprises cDNA from pooled tissue samples from ca. 15 embryos. The experimental details have been discussed with Sean May et al. at NASC. Experimenter name = Stuart Casson and Matthew Spencer; Experimenter phone = 0191 374 7356; Experimenter fax = 0191 374 2417; Experimenter institute = Durham University; Experimenter address = Integrative Cell Biology Laboratory; Experimenter address = School of Biological Sciences; Experimenter address = Durham University; Experimenter address = South Road; Experimenter address = Durham; Experimenter zip/postal_code = DH1 3LE; Experimenter country = UK Experiment Overall Design: 27 samples were used in this experiment
2008-06-14 | E-GEOD-5730 | 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 Experiment Overall Design: 18 samples were used in this experiment
2008-06-15 | E-GEOD-6825 | biostudies-arrayexpress
Project description:Arabidopsis has two genes, Arabidillo-1 and -2, related to animal Armadillo/ beta-catenin (Coates, 2003). Armadillo/beta-catenin directly activates the expression of developmental and cell proliferation genes, and also independently regulates cell-cell adhesion. Arabidillo proteins are nuclear and promote lateral root development. We aim to identify candidate Arabidillo target genes by comparing the transcriptomes of wild type, arabidillo-1/2 mutant and Arabidillo-1 overexpressing lines. The experiment will compare Col-0 (3 slides) with a 35S::Arabidillo-1-YFP overexpressing line (3 slides) and Col-3 with the arabidillo-1/2 mutant (3 slides). Each RNA prep will be from plate-grown 7-day old seedlings. Reference: Coates, JC (2003) Armadillo repeat proteins: beyond the animal kingdom? Trends in Cell Biology 13 p.463-471; Experimenter name: Juliet Coates; Experimenter phone: 0121 414 5481; Experimenter institute: University of Birmingham; Experimenter address: School of Biosciences; Experimenter address: Birmingham; Experimenter zip/postal_code: B15 2TT; Experimenter country: UK Experiment Overall Design: 12 samples were used in this experiment
2008-06-15 | E-GEOD-6826 | 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 Experiment Overall Design: 6 samples were used in this experiment
2008-06-15 | E-GEOD-6824 | biostudies-arrayexpress