Transcription profiling of Arabidopsis to compare change in ploidy level
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Nottingham Arabidopsis Stock Centre (NASC)
PROVIDER: E-GEOD-6828 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:By reciprocally crossing 2x and 4x C24 ecotype plants, we have generated 4 types of offspring with various ploidy (2x; 3x; 4x) or parent-of-origin genome dosage (3x from 4xper2x; 3x from 2xper4x). For each offspring generated, total RNA was extracted using Trizol from 8 seedlings 9 days after germination (developmental stage1.02, 2 leaves). Sample names: DIP diploid TET tetraploid TFE triploid female excess TME triplod male excess Experimenter name: Olivier Garnier Experimenter phone: 00-353-21-490-4028 Experimenter address: Plant molecular genetics lab, Dpt of Biochemistry, UCC Experimenter address: Lee Maltings Prospect row Experimenter zip/postal_code: Cork Experimenter country: Ireland Keywords: strain_or_line_design
2007-01-22 | GSE6828 | GEO
Project description:By reciprocally crossing 2x and 4x C24 ecotype plants, we have generated 4 types of offspring with various ploidy (2x; 3x; 4x) or parent-of-origin genome dosage (3x from 4xper2x; 3x from 2xper4x). For each offspring generated, total RNA was extracted using Trizol from 8 seedlings 9 days after germination (developmental stage1.02, 2 leaves). Sample names:
2007-03-29 | E-NASC-73 | biostudies-arrayexpress
Project description:Heterosis occurs where F1 offspring display superior characteristics to the parents. Heterosis is usually considered to result from crosses of genetically distinct (e.g. homozygous inbred) parents producing heterozygous F1 offspring. Most mechanistic models for heterosis require genetically heterozygous F1 hybrid offspring harbouring allelic diversity. Epigenetic or dosage models for heterosis could allow for heterosis effects in F1 offspring that display no allelic diversity with their parents. Reciprocal inter-ploidy crosses between diploid (2x) and tetraploid (4x) lines in the same genetic background generates genetically identical F1 triploids (3x). Such reciprocal F1 triploids differ according to whether the additional chromosome set is either maternally (maternal excess) or paternally inherited (paternal excess). Biomass accumulation and abiotic stress tolerance between the parental (2x and 4x) and reciprocal F1 triploid (3x) offspring of Arabidopsis thaliana accession C24 reveals a strong parental genome-dosage induced heterosis in the paternal-excess triploid F1 plants. In these F1 triploids, the circadian clock related genes CCA1 and TOC1, and the growth factors PIF4 and PIF5, display different expression levels compared to the non-heterotic maternal excess F1 triploid siblings. Whole transcriptome profiling reveals a paternal genome dosage effect on gene expression levels with strong enrichment for dysregulated abiotic stress-related genes in the paternal excess F1 triploids. This study demonstrates that heterosis can be triggered without allelic diversity in F1 triploid plants. Heterosis without heterozygosity in plants can be induced via an epigenetic “chromosome imprinting” like parental genome dosage effect requiring paternal transmission of an additional chromosome set
2014-08-01 | GSE52885 | GEO
Project description:Heterosis occurs where F1 offspring display superior characteristics to the parents. Heterosis is usually considered to result from crosses of genetically distinct (e.g. homozygous inbred) parents producing heterozygous F1 offspring. Most mechanistic models for heterosis require genetically heterozygous F1 hybrid offspring harbouring allelic diversity. Epigenetic or dosage models for heterosis could allow for heterosis effects in F1 offspring that display no allelic diversity with their parents. Reciprocal inter-ploidy crosses between diploid (2x) and tetraploid (4x) lines in the same genetic background generates genetically identical F1 triploids (3x). Such reciprocal F1 triploids differ according to whether the additional chromosome set is either maternally (maternal excess) or paternally inherited (paternal excess). Biomass accumulation and abiotic stress tolerance between the parental (2x and 4x) and reciprocal F1 triploid (3x) offspring of Arabidopsis thaliana accession C24 reveals a strong parental genome-dosage induced heterosis in the paternal-excess triploid F1 plants. In these F1 triploids, the circadian clock related genes CCA1 and TOC1, and the growth factors PIF4 and PIF5, display different expression levels compared to the non-heterotic maternal excess F1 triploid siblings. Whole transcriptome profiling reveals a paternal genome dosage effect on gene expression levels with strong enrichment for dysregulated abiotic stress-related genes in the paternal excess F1 triploids. This study demonstrates that heterosis can be triggered without allelic diversity in F1 triploid plants. Heterosis without heterozygosity in plants can be induced via an epigenetic “chromosome imprinting” like parental genome dosage effect requiring paternal transmission of an additional chromosome set 4 or 5 biological replicates per ploidy level, each replicate being a single two weeks old seedling
2014-08-01 | E-GEOD-52885 | 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 Experiment Overall Design: 6 samples were used in this experiment
2008-06-15 | E-GEOD-6827 | 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:In our laboratory we are interested in studying the functions of WRKY zink finger type transcription factors. There are 74 members of this gene family in Arabidopsis. WRKY factors are key regulators of distinct plant defense responses and are involved in certain developmental programs e.g. plant senescence. We would like to determine the functions of a small sub-group (group II-a) of WRKY factors. Our aim to compare and contrast the gene expression profiles of 35 days-old untreated wild type and WRKY T-DNA knockout plants grown in a growth chamber under long day growth conditions. All plants chosen at this stage showed slight yellowing of the first two to four leaves. Experimenter name: Bekir Uelker; Experimenter phone: 49-221-5062-310; Experimenter fax: 49-221-5062-353; Experimenter department: Somsissich Lab; Experimenter institute: Max-Planck-Institute for Plant Breeding Research; Experimenter address: Department of Plant Microbe Interactions; Experimenter address: Carl-von-Linne-Weg 10; Experimenter address: Cologne; Experimenter zip/postal_code: 50829; Experimenter country: Germany Experiment Overall Design: 8 samples were used in this experiment
2008-06-15 | E-GEOD-6830 | biostudies-arrayexpress
Project description:In our laboratory we are interested in studying the functions of WRKY zinc finger type transcription factors. There are 74 members of this gene family in Arabidopsis. WRKY factors are key regulators of distinct plant defense responses and are involved in certain developmental programs e.g. trichome development and plant leaf senescence. We would like to determine the functions of a small sub-group (group II-a) of WRKY factors in response to bacterial infection. Our aim is to compare and contrast the gene expression profiles of 3-week-old wild type and WRKY T-DNA knockout mutants grown in a growth chamber under long day growth conditions and subsequently challenged for 6 hours with the virulent bacterial pathogen /Pseudomonas syringae/ DC3000. Experimenter name: Bekir Uelker; Experimenter phone: 49-221-5062-310; Experimenter fax: 49-221-5062-353; Experimenter department: Somsissich Lab; Experimenter institute: Max-Planck-Institute for Plant Breeding Research; Experimenter address: Department of Plant Microbe Interactions; Experimenter address: Carl-von-Linne-Weg 10; Experimenter address: Cologne; Experimenter zip/postal_code: 50829; Experimenter country: Germany Experiment Overall Design: 7 samples were used in this experiment
2008-06-15 | E-GEOD-6829 | 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