Evaluation of performance of Arabidopsis Pathoarray 464_001: comparison with ATH1
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE4632 | GEO | 2006/04/08
SECONDARY ACCESSION(S): PRJNA95533
REPOSITORIES: GEO
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Project description:Expression profiling of wild-type plants and mutants with defects in key components of the defense signaling network was used to model the Arabidopsis network 24 hours after infection by Pseudomonas syringae pv. maculicola strain Psm ES4326. Results using the Affymetrix ATH1 array revealed that expression levels of most pathogen-responsive genes were affected by mutations in coi1, ein2, npr1, pad4, or sid2. These five mutations defined a small number of different expression patterns displayed by the majority of pathogen-responsive genes. P. syringae pv. tomato strain Pst DC3000 elicited a much weaker salicylic acid response than Psm ES4326. Additional mutants were profiled using a custom array. Profiles of pbs3 and ndr1 revealed major effects of these mutations and allowed PBS3 and NDR1 to be placed between the EDS1/PAD4 node and the SA synthesis node in the defense network. Comparison of coi1, dde2, and jar1 profiles showed that many genes were affected by coi1, but very few were affected by dde2 or jar1. Profiles of coi1 plants infected with Psm ES4326 were very similar to those of wild-type plants infected with bacteria unable to produce the phytotoxin coronatine, indicating that essentially all COI1-dependent gene expression changes in this system are caused by coronatine. This experiment consists of three biological replicates. For each genotype, two leaves per plant were pooled from three pots to prepare total RNA.
2008-07-18 | E-GEOD-11009 | biostudies-arrayexpress
Project description:Expression profiling of wild-type plants and mutants with defects in key components of the defense signaling network was used to model the Arabidopsis network 24 hours after infection by Pseudomonas syringae pv. maculicola strain Psm ES4326. Results using the Affymetrix ATH1 array revealed that expression levels of most pathogen-responsive genes were affected by mutations in coi1, ein2, npr1, pad4, or sid2. These five mutations defined a small number of different expression patterns displayed by the majority of pathogen-responsive genes. P. syringae pv. tomato strain Pst DC3000 elicited a much weaker salicylic acid response than Psm ES4326. Additional mutants were profiled using a custom array. Profiles of pbs3 and ndr1 revealed major effects of these mutations and allowed PBS3 and NDR1 to be placed between the EDS1/PAD4 node and the SA synthesis node in the defense network. Comparison of coi1, dde2, and jar1 profiles showed that many genes were affected by coi1, but very few were affected by dde2 or jar1. Profiles of coi1 plants infected with Psm ES4326 were very similar to those of wild-type plants infected with bacteria unable to produce the phytotoxin coronatine, indicating that essentially all COI1-dependent gene expression changes in this system are caused by coronatine.
2008-07-18 | GSE11009 | GEO
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 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 profiling by array 24 samples were used in this experiment
2009-11-17 | E-GEOD-18978 | biostudies-arrayexpress
Project description:The goal of the microarray was to compare the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326 (Psm)-induced transcriptome changes in the systemic leaves of the wild-type Col-0, lecrk-VI.2-2, and bak1-5 plants. Results showed that local Psm inoculation induced dramatic transcriptional changes in Col-0, with 564 and 151 genes up- and down-regulated at least twofold with a low q value (≤ 0.05), respectively. However, only 55 and 26 genes in lecrk-VI.2-2 and 221 and 121 genes in bak1-5 were up- and down-regulated, respectively. The majority of the genes that were induced or suppressed twofold or more with a low q value (≤ 0.05) in Col-0 were induced or suppressed to a smaller extent in bak1-5 and the smallest extent in lecrk-VI.2-2. These results indicate that both lecrk-VI.2-2 and bak1-5 suppressed Psm-induced systemic signaling with the lecrk-VI.2-2 mutation having a stronger effect than bak1-5.
2019-10-29 | GSE121886 | GEO
Project description:MgSO4 is given to prevent preterms neurological deficits. We have investigated proper effects and hypoxia-ischemia interfering effects of MgSO4 on transcription in neonate mice at day 5 (a brain development stage mimicking preterm maturity), at neuroprotection dose (600 mg/kg). Pools of RNA from 6 forebrains (3 males and 3 females) were used for total RNA extraction at 5 times post single MgSO4 injection (1.5H, 3H, 6H, 12H, 24H). Separately, MgSO4 effects were assessed post hypoxia-ischemia (3H and 12H). Co-hybridization of MgSO4-treated mRNA (labelled Cy5) and control tissues mRNA (labelled Cy3) were performed on Agilent (design 026655) micro-arrays in 4-7 replicates. Co-hybridization of saline injected (Labelled Cy3) or MgSO4 injected (Labelled Cy5) hypoxia-ischemia (according to Rice Vannucci (RV) procedure) exposed mice brains were performed on Aglient (design 026655) microarrays in triplicates.
2021-04-16 | GSE144455 | GEO
Project description:Wild type zebrafish (AB strain, https://zfin.org/action/genotype/view/ZDB-GENO-960809-7) were set up for mating overnight, in 3:2 ratios, females and males, respectively. Fertilized embryos from wildtype zebrafish AB strain were used for all experiments and kept in Embryo medium (E3, 5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4) in an incubator at 28ºC. At 1dpf, larvae were manually dechorionated under a stereomicroscope. At 2dpf, zebrafish larvae were divided randomly into the different experimental groups, at a density of 12 larvae per well of a 12 well plate (Corning) in 1.5mL of E3. Three biological replicates of 12 larvae per condition were exposed to different conditions for 4 hours at 28 ºC: DMSO; DMSO + CH223191 (5mM); 3-o-C12-L-HSL (50mM); 3-o-C12-L-HSL (50mM) + CH223191 (5 mM ); 1-hydroxyphenazine (1-HP, 5mM); 1-HP (5mM) + CH223191(5mM) and 1-HP (5mM) + 3-o-C12-L-HSL (50mM).To mention, in experiments using the Aryl hydrocarbon Receptor inhibitor CH223191, larvae were pre-exposed to 5uM of the inhibitor for 2h prior to the start of the experiment and the inhibitor was kept during the experiment. After the desired exposure to diverse ligands, larvae were euthanized with Tricaine (MS-222, 300 µg/mL) and placed in Trizol for RNA isolation. The same experimental layout was performed 5 times, and samples were subjected to microarray hybridization and analysis.
2019-10-01 | GSE121101 | GEO
Project description:To determine the genes that change mRNA transcript abundance in primary human keratinocytes treated by S. aureus phenol-soluble modulins (PSM), we stimulated keratinocytes for 24h with either DMSO(-) Ctl or synthetic PSMα3 (5μg/mL).
2019-03-05 | GSE124818 | GEO
Project description:Expression analysis was performed with two TDNA insertion mutants of taf4b i.e; taf4bprm (TDNA insertion in promoter region) and taf4bint (TDNA insertion in intronic region), Taf4b overexpression lines, taf4bprmcpr5 double mutant lines (Double mutant was generated by crossing taf4bprm with cpr5) and Col-0 in normal condition as well as with taf4bprm mutant and Col-0 infected with fungi AB (Alternaria brassicicola) and bacteria ES4 (Pseudomonas syringae pv.maculicola ES4326 ) in different perspectives. Affymatrix expression analysis was executed to provide mechanistic details of regulation of genes by Taf4b in plants.
2016-12-01 | GSE45690 | GEO
Project description:Target capture by NRX1, NRX1(C58,378S) containing columns versus a control column. Recombinant NRX1 and mutant NRX1(C58,378S) proteins were immobilised on NHS-activated beads. Proteins were extracted from Arabidopsis plants treated for 24hrs with Pseudomonas syringae ES4326 and put through the columns. Proteins were eluted from columns using DTT.
2016-12-18 | MSV000080429 | MassIVE