Project description:The effect of the overexpression of Plant Cysteine Oxidase (PDCO1) on the transcriptome of Arabidopsis resettes was investigated with plants subjected to a 4h hypoxia (5% O2 v/v in air). For this purpose, 4-week old rosette of wild-type and 35S:FLAG:CDO1 plants were compared. Samples were composed of pools of 5 plants. In total, 6 samples were analyzes, subdivided in 2 thesis with 3 replicates each. 35S:PCO1 plants (treated with hypoxia) were compared to wild-type plants (treated with hypoxia).
Project description:The effect of the overexpression of Plant Cysteine Oxidase (PCO1) on the transcriptome of Arabidopsis rosettes was investigated. For this purpose, 4-week old rosette of wild-type and 35S:FLAG:CDO1 plants were compared. Samples were composed of a pool of 5 plants. In total, 6 samples were analyzes, subdivided in 2 thesis with 3 replicates each. 35S:PCO1 plants were compared to wild-type plants.
Project description:In this study we analyzed the effect of overexpression of an HA-tagged version of the ERF RAP2.12 on the transcriptome levels in aerobic and hypoxic-treated (O2 21% and 1%, respectively) Arabidopsis thaliana rosettes. We also analyzed the effect of a RAP2.12 and RAP2.2 simultaneous silencing in aerobic and hypoxic-treated (O2 21% and 1%, respectively) Arabidopsis thaliana rosettes. We treated Arabidopsis Col-0 (wt) rosettes and transgenic HA::RAP2.12 and amiRAP2.2-12 , 5-week old, grown in 8/16 light/dark photoperiod with: -Control (22°C, dark, 21% O2, 1.5h). -Hypoxia (22°C, dark, 1% O2, 1.5h).
Project description:Arabidopsis nudix hydrolase 7 knock-out mutant Atnudt7-1 exhibits a reduced size phenotype when compared with age-matched Col-0 wildtype plants growing in potting mix of 12 parts vermiculite: 3 parts redi-earth and 1 part sand. In these array experiments the differences in gene expression caused by this mutation is assessed in comparison to wildtype plants.
Project description:In this experiment we used leaves from 6-week-old Arabidopsis SDH1-1/sdh1-1 mutant and Wt plants (Ws). The leaves were collected in the middle of light period.
Project description:This study profiles transcriptomic changes of Arabidopsis thaliana Col-0 in response to submergence. This dataset includes CEL files, RMA signal values and MAS5 P/M/A calls from total mRNA populations of plants at 9 to 10 leaf rosette stage. Biological replicates of root and shoot tissues were harvested after 7 h and 24 h of submergence in darkness along with corresponding non-submerged dark controls. To characterize the dark response, non-submerged light controls plants were harvested at the 0 h time point. Quantitative profiling of cellular mRNAs was accomplished with the Affymetrix ATH1 platform. Changes in the transcriptome in response to submergence and early darkness were evaluated, and the data led to identification of genes co-regulated at the conditional and organ-specific level. 20 samples, 5 conditions (7 h submergence in darkness, 7 h darkness, 24 h submergence in darkness, 24 h darkness, 0 h light control), 2 RNA pools (rosette leaf and root tissues), 2 independent biological replicate experiments
Project description:This SuperSeries is composed of the following subset Series: GSE35057: Phytochrome Interacting Factor 4 and 5 regulate different set of genes in high and low red/far-red light GSE35059: ChIP-Seq analysis of Phytochrome Interacting Factor 5 DNA binding in low R/FR condition Refer to individual Series
Project description:Detailed information: Rice (*Oryza sativa* L. cv. Nipponbare) is a drought-susceptible species which is well suited for studies of abiotic stress response because of the comprehensive bioinformatics resource available. By withholding water from the entire root system of young rice plants, or half the root system only, it was possible to infer the relative impact of signals arriving from roots growing in wet and dry soil on the shoot proteome. The global proteome of shoots had 685 proteins in common to all three drought treatments but there were major shifts in abundance of individual proteins within 16 functional categories. The dominant changes were analyzed more deeply. First, we investigated transport and cell component organization, where some proteins were up-regulated by drought but many more down-regulated. Proteins involved in protein metabolism were up-regulated in general by drought when they were responsible for protein degradation but those involved in protein synthesis were down-regulated when water was withheld. Stress-related proteins behaved very consistently by increasing in droughted plants but notably some proteins were most abundant when roots of the same plant were growing in both wet and dry soil. This suggests that drought signals are complex interactions and not simply the additive effect of water supply to the roots. Changes in carbohydrate-processing proteins were consistent with the passive accumulation of soluble sugars in shoots under drought, with hydrolysis of sucrose and starch synthesis both enhanced. Data analysis information: The result raw files were converted to mzXML format and processed through the global proteome machine (GPM) software (version 2.1.1) of the X!Tandem algorithm (freely available at http://www.thegpm.org). The 16 gel fractions were processed serially for each experiment and the output files were generated as non-redundant, merged files with protein identifications with log (e) values less than -1, for each individual gel fraction. A protein database compiled from NCBI *O*. *sativa* with 26938 protein sequences (August 2011) was used in GPM to search the tandem mass spectra; the database also included common trypsin and human peptide contaminants. False discovery rates (FDR) were evaluated by searching against a reversed sequence database. Search parameters included MS and MS/MS tolerances of +2 Da and +0.2 Da, carbamidomethylation of cysteine as fixed modifications, oxidation of methionine as variable modifications and tolerance of two missed tryptic cleavages and K/R-P cleavages.