Arabidopsis thaliana mutant leaves treated with Pseudomonas syringae ES4326
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Raka Mitra
PROVIDER: E-GEOD-18978 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:In order to better understand the transcriptional networks triggered by pathogen inoculation, we monitored gene expression in leaves of mutant Arabidopsis plants, inoculated with Pseudomonas syringae ES4326 and wild type Col-0 plants grown in parallel. Individual leaves were injected in the morning using a needle-less syringe with 10E5 cfu cm-2 PsmES4326 (suspended in 5 mM MgSO4). For the wild type, leaves were also mock treated with 5 mM MgSO4. Leaves were harvested 24 hours later. Plants were grown in pots with BM-2 soil (Berger Peat Moss Ltd, Quebec, Canada) at a density of 9 plants per pot and kept at 22 degrees Celsius with 75% humidity and a 12 hour day length. Keywords: Expression profilling by array
2009-11-18 | GSE18978 | GEO
Project description:In starchless mutants of Arabidopsis, pgm, and wild type, Col0, there are small differences in transcript levels at the end of the day, but large differences at the end of the night. Many of the transcripts of genes involved in biosynthesis and growth are repressed in the pgm mutant (Thimm et al., 2004). It is hypothesized that a transient depletion in sugars at the end of the night inhibits carbon utilization at the beginning of the day (Gibon et al., 2004). In order to test if the same inhibition of transcripts involved in biosynthesis and growth also occurs in starch excess mutants of Arabidopsis, Affymetrix arrays will be generated for WT (Col0), and the following mutants: sex4-3 (Salk 102567), ptpkis2 (Salk 053285), and sex1-3 (Yu et al., 2001). WT, sex4-3, and ptpkis2 plants were grown for 30 days and sex1-3 plants were grown for 36 days. All plants were grown in a growth chamber with a 12 hour photoperiod, quantum flux 100 mol m-2s-1, relative humidity was at least 75%, and a constant temperature of 20oC. Three leaves from 8 different plants of each genotype were harvested using a green safe lamp 0.5 hours before the lights came on in the morning and immediately frozen in LN2. Leaf material was powered using a mortar and pestle and RNA was extracted using a Purescript RNA isolation kit (Gentra Systems, MN, USA). Samples were then treated with DNaseI (Invitrogen, CA, USA). 12 samples were used in this experiment.
2009-12-04 | E-GEOD-19260 | biostudies-arrayexpress
Project description:In order to protect themselves from pathogens, plants activate a battery of defense pathways, many of which involve changes in gene expression. We are interested in identifying plant genes that are differentially expressed in response to pathogen exposure, with the ultimate goal of studying the roles of these genes in plant defense. Experiment Overall Design: Whole plants are grown in soil, and individual leaves from 3-4 week old plants are injected with a bacterial suspension, or a mock (5mM MgSO4) control. Approximately five leaves are harvested 24 hours after inoculation and used for RNA preparation, labeling and Affymetrix hybridization.
2008-06-13 | E-GEOD-4429 | biostudies-arrayexpress
Project description:We used N-(1-naphthyl) phthalamic acid (NPA)-induced vascular overgrowth in Arabidopsis leaves to look for differential up-regulation of genes in NPA-treated tissues that may be involved in vascular differentiation. Arabidopsis thaliana Col-0 plants were grown for approximately 2 weeks on solid ATS medium (1) containing a final concentration of 10 um NPA (dissolved in DMSO) or an equivalent volume of DMSO (control). At this stage plants had approximately 6 rosette leaves. RNA was prepared from entire shoot tissues of control (DMSO) or NPA-treated plants.(1) Lincoln et al., 1990. Plant Cell 2: 1071-1080. 2 samples were used in this experiment.
2009-12-05 | E-GEOD-19262 | biostudies-arrayexpress
Project description:In plant axillary bud dormancy and outgrowth are regulated by phytohormones, but it is still unknown about its molecular mechanism. We reveal that Arabidopsis axillary buds located at axil of rosette leaves show dormancy and that this is broken by the decapitation of main stem, resulting in the bud outgrowth. To investigate about the molecular mechanisms of dormancy and outgrowth, we carried out gene expression analysis during axillary shoot outgrowth in Arabidopsis wild type Columbia accession. Since axillary buds did not initiate outgrowth (dormancy) at 5 day after bolting of main stem, we used 5-day bolted plants as a control (before decapitation). Then, main stems were decapitated, and axillary shoots were collected at 24 hours after decapitation (named as growing shoot). Total RNA was prepared from either control or growing shoots and used for the microarray analysis. We carried out duplicate microarray analysis using independent plant materials.Ref):Tatematsu et al., Plant Physiol. 138: 757-766 (2005). Keywords: Expression profilling by array 4 samples were used in this experiment
2009-11-17 | E-GEOD-18987 | biostudies-arrayexpress
Project description:We used three different strains of Pseudomonas syringae pv tomato DC3000 to investigate systemic responses to infection in Arabidopsis and the development of SAR. Wildtype DC3000, the hrpA mutant and DC3000 carrying the avirulence gene avrRpm1 were syringe infiltrated into 4-week-old plants at a concentration of 10e8 cfu/ml. At least 5 leaves per plant were infiltrated and at least 10 plants were pooled for each sample. Systemic, uninfected tissue was then harvested at 8, 12 and 21h after inoculation. Three independent experiments were carried out to give three biological replicates for each timepoint. 27 samples were used in this experiment.
2009-12-09 | E-GEOD-19264 | biostudies-arrayexpress
Project description:A number of RNA encoding different functions have been detected in the plant vasculature. An RNase L inhibitor, similar to that present in humans have been identified in the phloem sap of cucurbits. We are interested in analyze the role of this putative inhibitor on the transcript levels that could be present in the vasculature and mainly in the phloem stream. For this purpose, we obtained an RLI T-DNA insertion mutant and generated A. thaliana overexpressing lines using the ORF of the two alleles found in the database. Keywords: Expression profilling by array 6 samples were used in this experiment
2009-11-17 | E-GEOD-18981 | biostudies-arrayexpress
Project description:Reference: De Vos and Jander, 2009 - Plant, Cell, and Environment Aim: Identification of genes responding to aphid saliva. Background: During feeding on phloem sap aphids repeatedly salivate into the sieve element. It is thought that compounds in aphid saliva play a role in sustainable feeding. These compounds may include proteins and small molecules, which can function as virulence factors. Growth conditions Plants: Seeds of wild-type Arabidopsis thaliana (Col-0) were obtained from the were kept in 0.1% Phytagar (Invitrogen, Carlsbad, CA) for 24 h at 4°C prior to planting on Cornell mix with Osmocoat fertilizer. Plants were grown in Conviron growth chambers in 20- x 40-cm nursery flats at a photosynthetic photon flux density of 200 mmol m-2 s-1 and a 16-h photoperiod. The temperature in the chambers was 23°C and the relative humidity was 50%. Plants were grown for 3 weeks and used in experiments before flowering. Aphids: All experiments were conducted with a tobacco-adapted red lineage of M. persicae. Aphids were raised on cabbage (Brassica oleracea) with a 16-h day (150 mmol m-2 s-1 at 24°C) and an 8-h night (19°C) at 50% relative humidity. Experimental set-up/treatment: Fifty aphids were allowed to feed from 50 µL artificial diet, containing sucrose and amino acids (Kim and Jander, 2007) between two layers of Parafilm. After 24 h, artificial diet from 20 aphids and control (0 aphids) diet cups was collected and infiltrated into leaves of intact Arabidopsis plants using a 1-mL syringe without the needle. Plants for control diet and aphid saliva containing diet were grown in the same pot to allow for a paired comparison. Eighteen leaves (3 leaves from 6 plants) treated with control and aphid saliva containing diet were harvested and immediately frozen in liquid nitrogen. This experiment was repeated 3 times to function as independent biological replicates. RNA extraction + processing: RNA was extracted using the Qiagen Plant RNeasy kit. RNA quality and quantity was assessed with an Agilent BioAnalyser 2100. Samples were processed by the Cornell Microarray facility. Whole genome gene expression profiling was done using Affymetrix ATH1 GeneChips. Data analysis: Raw data from the microarrays was normalized at probe-level using gcRMA algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system. Significance of gene expression was determined using the LIMMA (Smyth, 2004) program and raw p values of multiple tests were corrected using False Discovery Rate (FDR). 6 samples were used in this experiment
2009-11-11 | E-GEOD-18960 | biostudies-arrayexpress
Project description:This experiment was designed to identify transcripts which are changed in plants deficient for evolutionary conserved EST1B gene. A mutation in est1b leads to a constitutive up-regulation of a PAD4-dependent pathogen response pathway. To eliminate secondary effects of the constitutive pathogen response in est1b mutants we will analyze transcriptoms in plants in which lack PAD4. Keywords: Expression profilling by array 6 samples were used in this experiment
2009-11-17 | E-GEOD-18979 | biostudies-arrayexpress
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