Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA142935 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Plant mitochondria signal to the nucleus leading to altered transcription of nuclear genes by a process called mitochondrial retrograde regulation (MRR). MRR is implicated in metabolic homeostasis and responses to stress conditions. Transcriptional consequences on nuclear gene expression of mitochondrial perturbations were examined by a microarray analyses. Expression of 606 genes was altered by monofluoroacetate (MFA) inhibition of the TCA cycle in leaves of soil grown Arabidopsis plants in the dark for 10 hours. Functional gene category (MapMan) and cluster analyses showed that genes with expression levels affected by perturbation from MFA inhibition were most similarly affected by biotic stresses such as pathogens, not oxidative stresses. Overall, the data provide further evidence for the presence of mtROS-independent MRR signaling, and support the proposed involvement of MRR and mitochondrial function in plant responses to biotic stress.
2013-01-01 | GSE29268 | GEO
Project description:Mitochondrial dysfunction in Arabidopsis thaliana.
| PRJNA111163 | ENA
Project description:Inhibition of the mitochondrial electron transport chain by antimycin A in Arabidopsis thaliana
| PRJNA142959 | ENA
Project description:We provide evidence that 5-EU metabolic labeling of Arabidopsis RNAs can be used for pulse-chase experiments, which allowed us to determine Arabidopsis RNA half-lives genome-wide without chemical inhibition of transcription. Similar to BRIC-Seq, we performed 5-EU IP chase (ERIC)-Seq in seedlings of A. thaliana. Hierarchical clustering of gene expression values allowed us to define at least five clusters of mRNAs that exhibited distinct degradation kinetics. To determine the RNA half-lives of each group, we applied an exponential decay model and a locally weighted scatterplot smoothing (LOWESS) and calculated the time where the concentration was halved. It became obvious that the half-lives determined by ERIC-Seq are much shorter than the ones determined after treatment with cordycepin or actinomycin D, respectively. We found that genes belonging to cluster A exhibiting the shortest half-lives are enriched in genes transcribed into non-coding RNAs, stress-related genes, genes involved in hormonal pathways and the metabolism of polyamines, which are also involved in stress responses. On the contrary, genes from cluster E, which have the longest half-lives, are specifically enriched in genes responsible for mitochondrial and plastic functions as well as primary metabolism (such as the TCA cycle)
2018-10-31 | GSE118461 | GEO
Project description:Transcriptional profiling of Arabidopsis thaliana 12-days old seedlings comparing Col-0 wild type with transgenic plants with altered expression of dual-targetting plastid/mitochondrial organellar RNA-polymerase RPOTmp. Transgenic plants used for experiment were: overexpressor plants obtained by transformation of Col-0 WT plants with genetic constructs created in [Tarasenko et al., 2016] contained catalytic part of RPOTmp enzyme with transit peptides of RPOTm (mitochondrial) and RPOTp (plastid) by agrobacterial transformation; plants with complementation of RPOTmp functions in mitochondria or chloroplasts obtained from transformation of GABI_286E07 rpotmp knockout-mutant plants with genetic constructs created in [Tarasenko et al., 2016]. Goal was to determine the effects of RPOTmp knockout/overexpression on global Arabidopsis thaliana gene expression.
2023-12-25 | GSE251661 | GEO
Project description:Plant mitochondria signal to the nucleus leading to altered transcription of nuclear genes by a process called mitochondrial retrograde regulation (MRR). MRR is implicated in metabolic homeostasis and responses to stress conditions. Transcriptional consequences on nuclear gene expression of mitochondrial perturbations were examined by a microarray analyses. Expression of 606 genes was altered by monofluoroacetate (MFA) inhibition of the TCA cycle in leaves of soil grown Arabidopsis plants in the dark for 10 hours. Functional gene category (MapMan) and cluster analyses showed that genes with expression levels affected by perturbation from MFA inhibition were most similarly affected by biotic stresses such as pathogens, not oxidative stresses. Overall, the data provide further evidence for the presence of mtROS-independent MRR signaling, and support the proposed involvement of MRR and mitochondrial function in plant responses to biotic stress. Three independent (bio-replicate) experiments were done using three independent plant samples in the treatments. For each, approximately 30 plants were used for the treated sample and about 30 plants were used as the control sample. Plants were treated with 5 mM monofluoroacetate in 0.01% Tween 20 and incubated in the dark at room temperature (25C) for 6 hours. RNA was isolated from the inhibitor treated and control plants and used for microarray experiments. For each independent (bio-replicate) experiment, two microarrays were utilized using Cy3 and Cy5 dye-labeled samples and dye swapping was incorporated- 2 microarrays for each of 3 independent experiments (6 microarrays total).
2013-01-01 | E-GEOD-29268 | biostudies-arrayexpress
Project description:Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. The presented model is a new semi-quantitative mathematical model of the metabolism of Arabidopsis thaliana. The Petri net formalism was used to express the complex reaction system in a mathematically unique manner. To verify the model for correctness and consistency concepts of network decomposition and network reduction such as transition invariants, common transition pairs, and invariant transition pairs were applied. Based on recent knowledge from literature, including the Calvin cycle, glycolysis and citric acid cycle, glyoxylate cycle, urea cycle, sucrose synthesis, and the starch metabolism, the core metabolism of Arabidopsis thaliana was formulated. Each reaction (transition) is experimentally proven. The complete Petri net model consists of 134 metabolites, represented by places, and 243 reactions, represented by transitions. Places and transitions are connected via 572 edges.
2020-04-09 | MODEL1801090001 | BioModels
Project description:Polysome profiling in Arabidopsis thaliana over a 24-hour diurnal cycle
| PRJNA262639 | ENA
Project description:Transcript levels in Arabidopsis thaliana over a 24-hour diurnal cycle
| PRJNA262637 | ENA
Project description:The aim of this study was to analyze the impact of autotetraploidy on gene expression in Arabidopsis thaliana by comparing diploid versus tetraploid transcriptomes. In particular, this included the comparison of the transcriptome of different tetraploid A. thaliana ecotypes (Col-0 vs. Ler-0). The study was extended to address further aspects. One was the comparison of the transcriptomes in subsequent generations. This intended to obtain information on the genome wide stability of autotetraploid gene expression. Another line of work compared the transcriptomes of different diploid vs. tetraploid tissues. This aimed to investigate whether particular gene groups are specifically affected during the development of A. thaliana autotetraploids. Samples 1-8: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Col-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 9-12: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Ler-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 13-24: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Col-0 leaves (6th - 8th). The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 25-32: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Ler-0 leaves (6th - 8th). The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 33-36: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid vs. tetraploid Ler-0 seedlings from the second (F2) and third (F3) generation after induction, respectively. The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 37-40: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid vs. tetraploid Col-0 seedlings from the second (F2) and third (F3) generation after induction, respectively. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 41-44: Arabidopsis thaliana Col-0/Ler-0 diploid transcriptome. Transcriptional profiling and comparison of diploid Col-0 vs. diploid Ler-0 seedlings. The experiment was carried out with pedigree of esrablished lines. Samples 45-48: Arabidopsis thaliana Col-0/Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid Col-0 vs tetraploid Ler-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 and Ler-0 lines.
2010-05-01 | GSE18482 | GEO