Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA102967 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Selenate is chemically similar to sulfate and can be taken up and assimilated by plants via the same transporters and enzymes. In contrast to many other organisms, selenium (Se) has not been shown to be essential for higher plants. In excess, Se is toxic and restricts development. Both Se deficiency and toxicity pose problems worldwide. To obtain better insight into the effects of Se on plant metabolism and into plant mechanisms involved in Se tolerance, the transcriptome of Arabidopsis plants grown with or without selenate was studied, and Se-responsive genes identified. Roots and shoots exhibited different Se-related changes in gene regulation and metabolism. Many genes involved in sulfur (S) uptake and assimilation were upregulated. Accordingly, Se treatment enhanced sulfate levels in plants, but the quantity of organic S metabolites decreased. Transcripts regulating the synthesis and signaling of ethylene and jasmonic acid were also upregulated by Se. Selenate appeared to repress plant development, as suggested by the down-regulation of genes involved in cell wall synthesis and auxin-regulated proteins. The Se-responsive genes discovered in this study may help create plants that can better tolerate and accumulate Se, which may enhance the effectiveness of Se phytoremediation or serve as Se-fortified food. Experiment Overall Design: Arabidopsis thaliana (ecotype WS) plants were vertically grown on +/- 40 micromolar selenate MS medium. Root and shoot tissues of 10-day-old plants were seperated and used for RNA extraction and hybridization on Affymetrix microarrays. All conditions were duplicated.
2008-11-06 | E-GEOD-9311 | biostudies-arrayexpress
Project description:Selenate is chemically similar to sulfate and can be taken up and assimilated by plants via the same transporters and enzymes. In contrast to many other organisms, selenium (Se) has not been shown to be essential for higher plants. In excess, Se is toxic and restricts development. Both Se deficiency and toxicity pose problems worldwide. To obtain better insight into the effects of Se on plant metabolism and into plant mechanisms involved in Se tolerance, the transcriptome of Arabidopsis plants grown with or without selenate was studied, and Se-responsive genes identified. Roots and shoots exhibited different Se-related changes in gene regulation and metabolism. Many genes involved in sulfur (S) uptake and assimilation were upregulated. Accordingly, Se treatment enhanced sulfate levels in plants, but the quantity of organic S metabolites decreased. Transcripts regulating the synthesis and signaling of ethylene and jasmonic acid were also upregulated by Se. Selenate appeared to repress plant development, as suggested by the down-regulation of genes involved in cell wall synthesis and auxin-regulated proteins. The Se-responsive genes discovered in this study may help create plants that can better tolerate and accumulate Se, which may enhance the effectiveness of Se phytoremediation or serve as Se-fortified food. Keywords: selenate, abiotic stress
2007-10-24 | GSE9311 | GEO
Project description:Plant cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes involved in Cys biosynthesis and located in different subcellular compartments. These enzymes are made up of a complex variety of isoforms resulting in different subcellular Cys pools. To unravel the contribution of cytosolic Cys to plant metabolism, we characterized the knockout oas-a1.1 and osa-a1.2 mutants, deficient in the most abundant cytosolic OASTL isoform in Arabidposis thaliana. Total intracellular Cys and glutathione concentrations were reduced, and the glutathione redox state was shifted in favour of its oxidized form. Interestingly, the capability of the mutants to chelate heavy metals did not differ from that of the wild type, but the mutants have an enhanced sensitivity to Cd. With the aim of establishing the metabolic network most influenced by the cytosolic Cys pool, we used the ATH1 GeneChip for evaluation of differentially expressed genes in the oas-a1.1 mutant grown under non-stress conditions. The transcriptomic footprints of mutant plants had predicted functions associated with various physiological responses that are dependent on reactive oxygen species and suggested that the mutant was oxidatively stressed. To further elucidate the specific function(s) of the OAS-A1 isoform in the adaptation response to cadmium we extended the trasncriptome experiment to the wild type and oas-a1.1 mutant plants exposed to Cd. The comparison of transcriptomic profiles showed a higher proportion of genes with altered expression in the mutant than in the wild type, highlighting up-regulated genes identified as of the general oxidative stress response rather than metal-responsive genes. Wild type and oas-a1.1 mutant plants were grown hydroponically and, after a two-week acclimation period, the roots and shoots were harvested separately. Total RNA was then prepared and analyzed using the Affymetrix-Arabidopsis ATH1GeneChip array. Three biological replicates were performed for each sample. We made two different comparisons to classify the differently expressed genes in the mutant plant: oas-a1.1 roots versus wild-type roots and oas-a1.1 shoots versus wild-type shoots. Hydroponically-grown wild type and oas-a1.1 mutant plants were further treated with 50µM CdCl2 and 18h-treated-roots and 24h-treated-shoots were harvested. Total RNA was then prepared and analyzed using the Affymetrix-Arabidopsis ATH1GeneChip array. Three biological replicates were performed for each sample. Different comparisons were performed as follows: 18h Cd-treated wild type roots versus untreated wild type roots; 24h Cd-treated wild type shoots versus untreated wild type shoots; 18h Cd-treated oas-a1.1 roots versus untreated oas-a1.1 roots; 24h Cd-treated oas-a1.1 shoots versus untreated oas-a1.1 shoots; 18h Cd-treated oas-a1.1 roots versus 18h Cd-treated wild type roots; 24h Cd-treated oas-a1.1 shoots versus 24h Cd-treated wild type shoots
2010-10-01 | E-GEOD-19245 | biostudies-arrayexpress
Project description:Expression data from Arabidopsis roots and shoots grown with or without iron
| PRJNA172742 | ENA
Project description:Experiments were achieved on Arabidopsis thaliana. Transcriptional profiling of roots and shoots from plants treated with lead were compared to plants treated in similar conditions without lead. Four weeks old A. thaliana seedlings were treated in hydroponic cultures with Pb during 3 days, by adding or not 40 µM Pb(NO3)2.
2015-01-28 | GSE65333 | GEO
Project description:Plant hormones and small secretory peptides often function as environmental stress mediators. Some recent reports indicate that small secretory peptides, such as CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE), also function as mediators of environmental stimuli. CLE2 is induced in roots by light depriviation. Plants without functional CLE2 showed a chlorosis phenotype when grown under shade. Here, we identified specific genes downstream of CLE2 in roots and shoots with transformed Arabidopsis plants.
2020-12-31 | GSE149015 | GEO
Project description:Plant hormones and small secretory peptides often function as environmental stress mediators. Some recent reports indicate that small secretory peptides, such as CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE), also function as mediators of environmental stimuli. CLE３ is induced in roots by defense elicitor treatment. Plants without functional CLE3 showed compromized defense gene responses in shoots when plant roots were treated with NaSA. Here, we identified specific genes downstream of CLE3 in roots and shoots with transformed Arabidopsis plants.
2021-09-01 | GSE176064 | GEO
Project description:The goal of this project is to compare the primary metabolite profile in different tissue types of the model plant Arabidopsis thaliana. Specifically, plants were grown hydroponically under the long-day (16hr light/day) condition at 21C. Tissue samples, including leaves, inflorescences, and roots were harvest 4 1/2 weeks post sowing. Untargeted primary metabolites profiling was carried out using GCTOF.
2021-12-09 | ST002012 | MetabolomicsWorkbench
Project description:A silencing signal in plants with an RNA specificity determinant moves through plasmodesmata and the phloem. To identify the mobile RNA we grafted Arabidopsis thaliana shoots to roots that would be a recipient for the silencing signal. Using high throughput sequencing as a sensitive detection method and mutants to block small RNA (sRNA) biogenesis in either source or recipient tissue, we detected endogenous and transgene specific sRNA that moved across the graft union. Surprisingly we found that the mobile endogenous sRNAs account for a substantial proportion of the sRNA in roots and we provide evidence that 24nt mobile sRNAs direct epigenetic modifications in the genome of the recipient cells. Mobile sRNA thus represents a mechanism for transmitting the specification of epigenetic modification and could affect genome defence and responses to external stimuli that have persistent effects in plants. Keywords: Small RNA Analysis, Epigenetics
2010-03-24 | GSE20663 | GEO
Project description:Gene expression profiles of roots and shoots of WT and NIC3 OX plants under control and 5 days rought-stressed conditions were analyzed using the custom microarray (GPL19830).
2021-12-01 | GSE162310 | GEO