Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA98603 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Phloem-feeding pests cause extensive crop damage throughout the world yet little is understood about how plants perceive and defend themselves from these threats. The silverleaf whitefly (SLWF; Bemisia tabaci type B) is a good model for studying phloem-feeding insect-plant interactions as SLWF nymphs cause little wounding and have a long, continuous interaction with the plant. Using the Arabidopsis ATH1 GeneChip, the global responses to Silverleaf Whitefly 2nd instar feeding were examined. Keywords: stress response
2006-12-15 | GSE6516 | GEO
Project description:geLC-MS/MS analysiswas performed to identify proteins that are present in apoplastic fluid isolated from rosette leaves of 8-week-old wild type and carbonic anhydrase (ca1ca4) mutant Arabidopsis plants.
2014-08-22 | PXD000692 | Pride
Project description:geLC-MS/MS analysis was performed to identify proteins that are present in apoplastic fluid isolated from rosette leaves of 8-week-old wild type and carbonic anhydrase (ca1ca4) mutant Arabidopsis. Plants were grown in either low (150 ppm) or high (500 ppm) CO2.
2014-08-22 | PXD000693 | Pride
Project description:Total and polyribosomal RNA was extracted from rosette leaves of 5-6-week-old wild-type and transgenic Arabidopsis plants (ecotype Col-0). After linear amplification using a modified Eberwine procedure, Cy3- or Cy5-labeled cDNA targets were produced from sense-strand RNA through reverse transcription Keywords: repeat sample
2005-06-06 | GSE2132 | GEO
Project description:Phloem-feeding pests cause extensive crop damage throughout the world yet little is understood about how plants perceive and defend themselves from these threats. The silverleaf whitefly (SLWF; Bemisia tabaci type B) is a good model for studying phloem-feeding insect-plant interactions as SLWF nymphs cause little wounding and have a long, continuous interaction with the plant. Using the Arabidopsis ATH1 GeneChip, the global responses to Silverleaf Whitefly 2nd instar feeding were examined. Experiment Overall Design: The silverleaf whitefly colony (Bemisia tabaci type B; Bemisia argentifolii Bellows and Perring) was maintained on Brassica napus cv. âFlorida broad leafâ grown under fluorescent and incandescent lights (180 μE m-2 s-1) 27°C with 55% relative humidity under long-day (16 hr light: 8 hr dark) conditions in the Insectory and Quarantine Facility at the University of California, Riverside. Adult whiteflies are collected from infested plants by aspiration into 15-ml falcon tubes. Experiment Overall Design: Individual Arabidopsis thaliana ecotype Columbia plants were grown for 21 days in 4-inch diameter, round pots under fluorescent and incandescent lights (180 μE m-2 s-1) with 50% relative humidity, 23° C and an 8 hr-light/16-hr dark cycle. One hundred adult whiteflies were collected into each 15-ml falcon tube and the tube was placed upright in each pot. Plants were individually encased with 5- by 10-inch nylon bags that were secured to each pot with a rubber band. The whiteflies were released by unscrewing the falcon tube. After seven days, the adult whiteflies were removed from the plants by aspiration. The infested and non-infested plants were caged for the remainder of the experiment to ensure any adults that escaped aspiration could not reach the plants. Rosette tissue was collected after 28 days, when 2nd and 3rd instars were observed on wild-type Columbia plants. Developmentally matched leaves were harvested from uninfested plants. Infestations were performed in two growth chambers; each chamber contained one replicate experiment, which included 10 control and 10 infested plants. This experiment was repeated for a total of 8 biological replicate experiments. Experiment Overall Design: Total RNA from the eight biological replicates was isolated using the RNAwiz protocol (Ambion Inc., Austin, TX) and purified using a RNAeasy column (Qiagen, Valencia, CA). RNA from the two biological replicates performed in each growth chamber were pooled to eliminate variance due to different environmental factors. This yielded the infested and control RNA pools used in the microarrays (Exp1 and Exp2) and RT-PCRs (Exp3 and Exp4). The quality of the RNA was determined by A260/A280 absorbance readings. RNA integrity (1 µg) was verified by fractionation on a 1% formaldehyde gel. Experiment Overall Design: Hybridization Experiment Overall Design: Biotin-labeled cRNAs were synthesized from infested and control RNAs for Exp1 and Exp2 at the UC Irvine Microarray Facility using the Affymetrix Eukaryotic One-Cycle Target Labeling Assay protocol (Affymetrix GeneChip Expression, Analysis Technical Manual, Affymetrix, Santa Clara, CA). The labeled cRNA was hybridized to Affymetrix Arabidopsis genome ATH1 Chip arrays, washed, and scanned using a Hewlett Packard Genearray scanner (Hewlett-Packard, Palo Alto, CA). Experiment Overall Design: MAS 5.0 was performed using the standard parameters (Affymetrix GeneChip Expression, Analysis Technical Manual, Affymetrix, Santa Clara, CA.) Genes with âabsentâ calls in replicate experiments were removed from further analysis.
2008-06-14 | E-GEOD-6516 | biostudies-arrayexpress
Project description:Differentially regulated genes in rosette leaves and roots of hydroponically grown Arabidopsis thaliana Col-0 and nrt1.5-5 mutant plants were identified by microarray analyses.
2017-02-28 | GSE60975 | GEO
Project description:Plants can cope with stress better if they experience a mild form of the stress before the actual \\"real\\" stress event. In Arabidopsis thaliana it is known that plants that harboured eggs of the White cabbage butterfly (Pieris brassicae) before larval feeding can defend better against the herbivore stress. The main aim of the experiment was to compare the priming effect induced by insect egg deposition of Pieris brassicae between vegetative and reproductive (first open flowers) Arabidopsis thaliana plants on the transcriptional level. We used a full factorial setup consisting of a) untreated control plants , b) plants which experienced eggs for 6 days without larval feeding after that period, c) plants which experienced no eggs before larval feeding for 24 hours d) plants which experienced eggs for 6 days and larval herbivory for 24 hours. This setup was conducted with 6 week old vegetative plants and 10 week old reproductive plants were the first flowers were open. For all treatments leaf tissue from the leaves that experienced egg oviposition and/or larval feeding were collected. From reproductive plants flower buds were collected as well.
2022-05-10 | E-MTAB-9196 | biostudies-arrayexpress
Project description:Nontargeted and targeted metabolomics measurements of abiotic stress responses in three-week-old Arabidopsis thaliana plants' rosette leaf tissue for Col-0 wild type plants and double/triple knockout mutants of aquaporins (pip2;1 pip2;2 and pip2;1 pip2;2 pip2;4) treated with drought, heat at different air humidities, or combined drought-heat stress at different air humidities. This experiment contains FT-ICR-MS measurements for 103 Arabidopsis thaliana rosette leaf samples covering three genotypes under six different environmental conditions. The three genotypes comprise the Col-0 wildtype and two loss-of-function mutants of aquaporins, a pip2;1 pip2;2 double mutant and a pip2;1 pip2;2 pip2;4 triple mutant (respective AGI locus identifiers: AT3G53420, AT2G37170, AT5G60660). The six conditions include control condition (well-watered, 22 °C, 70% relative air humidity), drought stress (one week without watering), heat stress without changing the absolute humidity of the ambient air (6 hours at 33 °C, 37% relative air humidity), heat stress with supplemented air humidity to maintain a constant vapor pressure deficit before and during the heat episode (6 hours at 33 °C, 84% relative air humidity), and the combinations of drought pretreatment with each of the two heat stress variants (one week of drought followed by 6 hours of heat stress). Samples from all conditions were harvested at the same time (within 15 min starting at 5 pm). For validation, GC-TOF-MS measurements were done for two genotypes (wildtype, double mutant) and two conditions (drought, control) on partially overlapping samples.
2017-07-17 | MTBLS355 | MetaboLights
Project description:Arabidopsis thaliana plants were grown from seeds in Petri dishes on MS medium. 4 days old plants were co-incubated with L. bicolor without physical contact. Roots were harvested after 0, 2, 4 and 7 days of co-incubation, rosette leaves were harvested after 4 days of co-incubation.
2020-12-10 | E-MTAB-8684 | biostudies-arrayexpress
Project description:We used microarrays to detail Arabidopsis gene expression in response to paraquat, a herbicide that acts as a terminal oxidant of photosystem I that in the light leads to the enhanced generation of superoxide and hydrogen peroxide inside plastids. Within a few hours after paraquat treatment changes in nuclear gene expression occur. Distinct sets of genes were activated that were different from those induced by another reactive oxygen species, singlet oxygen. Experiment Overall Design: Arabidopsis thaliana rosette leaves were harvested 1, 2, and 4 h after spraying either with a solution of 20 microM paraquat (methyl viologen, Sigma) in 0.1% Tween or with Tween alone for RNA extraction and hybridization on Affymetrix ATH1 microarrays. Plants were grown on soil for 3 weeks under continuous light at 90 mmol. m-2 . s-1. For each sample, the rosette leaves of five to six 3-week-old plants (before they start bolting) were collected for RNA extraction. Total RNAs from two separate biological experiments were pooled for the preparation of cDNA and the subsequent synthesis of biotin-labeled complementary RNA as recommended by Affymetrix.
2008-04-08 | E-GEOD-10464 | biostudies-arrayexpress