Arabidopsis thaliana
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ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-32566
PROVIDER: PRJNA147125 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Exogenous Sulfide Reverses the Alteration of Transcriptional Profiling of the des1-1 Mutant (Arabidopsis thaliana)
2015-12-04 | E-GEOD-32566 | ExpressionAtlas
Project description:Arabidopsis thaliana cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes that catalyze the biosynthesis of cysteine. Recently, we have deeply investigated about one of the minor OASTL-like protein located in the cytosol, named DES1, highlighting some important clues about its metabolic function. We have demonstrated that DES1 catalyzes the desulfuration of L-cysteine to sulfide plus ammonia and pyruvate, instead of the biosynthesis of Cys, and thus, is a novel L-cysteine desulfhydrase (EC 4.4.1.1). The functionality of DES1 is being revealed by the phenotype of the T-DNA insertion mutants des1-1 and des1-2. We have performed a comparative transcriptomic analysis on leaves of the des1-1 and Col-0 wild type plants grown for 30 days under long-day conditions. The normalized data from the replicates showed differential expression of 1614 genes in the des1-1 mutant, with 701 genes down-regulated and 913 genes up-regulated by more than twofold, with a False Discovery Rate (FDR) of < 0.05 and an intensity signal restriction of lgSignal >7. This des1-1 transcriptional profile show a strong alteration when compared to a previous comparative transcriptomic analysis performed on leaves of the des1-1 and Col-0 wild type plants grown for 20 days under identical long-day conditions (GSE 19244). We have also performed a comparative transcriptomic analysis on leaves of the des1-1 and Col-0 wild type plants grown for 20 days and treated with sodium sulfide for 10 additional days. The comparison of the transcriptional profile of des1-1+Na2S versus Col-0+Na2S clearly shows that exogenous sulfide reversed the transcriptional level differences between the mutant and the wild type to reach similar transcriptional patterns as the array GSE19244. Our results suggest a role of sulfide as transcriptional regulator in the des1-1 mutant background.
2013-04-25 | GSE32566 | GEO
Project description:Arabidopsis thaliana cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes that catalyze the biosynthesis of cysteine. Recently, we have deeply investigated about one of the minor OASTL-like protein located in the cytosol, named DES1, highlighting some important clues about its metabolic function. We have demonstrated that DES1 catalyzes the desulfuration of L-cysteine to sulfide plus ammonia and pyruvate, instead of the biosynthesis of Cys, and thus, is a novel L-cysteine desulfhydrase (EC 4.4.1.1). The functionality of DES1 is being revealed by the phenotype of the T-DNA insertion mutants des1-1 and des1-2. We have performed a comparative transcriptomic analysis on leaves of the des1-1 and Col-0 wild type plants grown for 30 days under long-day conditions. The normalized data from the replicates showed differential expression of 1614 genes in the des1-1 mutant, with 701 genes down-regulated and 913 genes up-regulated by more than twofold, with a False Discovery Rate (FDR) of < 0.05 and an intensity signal restriction of lgSignal >7. This des1-1 transcriptional profile show a strong alteration when compared to a previous comparative transcriptomic analysis performed on leaves of the des1-1 and Col-0 wild type plants grown for 20 days under identical long-day conditions (GSE 19244). We have also performed a comparative transcriptomic analysis on leaves of the des1-1 and Col-0 wild type plants grown for 20 days and treated with sodium sulfide for 10 additional days. The comparison of the transcriptional profile of des1-1+Na2S versus Col-0+Na2S clearly shows that exogenous sulfide reversed the transcriptional level differences between the mutant and the wild type to reach similar transcriptional patterns as the array GSE19244. Our results suggest a role of sulfide as transcriptional regulator in the des1-1 mutant background. Using the Affymetrix ATH1 GeneChips, we performed two comparative transcriptomic analyses on leaves of the des1-1 and Col-0 wild type plants grown on soil under long-day conditions. One was performed on plants grown for 30 days and the other on plants grown for 20 days and treated for 10 additional days with 200 mM Na2S. Three biological replicates were performed for each sample and hybridized to the chips. We made the comparison of des1-1 versus wild-type and des1-1+Na2S versus wild-type+Na2S to classify the differently expressed genes in the mutant plant.
2013-04-25 | E-GEOD-32566 | biostudies-arrayexpress
Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.
2018-11-14 | ST001096 | MetabolomicsWorkbench
Project description:Cadmium sulfide quantum dots (CdS QDs) are widely used in novel equipment. The relevance of the research lies in the need to develop risk assessments for nanomaterials, using as basis a model plant species. Here a screen of Arabidopsis thaliana mutant lines was performed in an attempt to identify plants tolerant to CdS QDs. Two tolerant Ds insertion mutant lines (atnp01 and atnp02) were identified. A whole-genome microarray experiment showed how genes were regulated by CdS QDs. Most of the genes involved in the response to CdS QDs were related to detoxification and general metabolism. The two mutant lines treated with CdS QDs showed different patterns of gene expression.
2014-06-15 | GSE53989 | GEO
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
Project description:This study evaluates the effects of exogenous auxin on the Arabidopsis thaliana root proteome at 8, 12, and 24 hours post-treatment.
2017-07-18 | PXD001400 | Pride
Project description:How bacteria from the microbiota modulate the physiology of its host is an important question to address. Previous work revealed that the metabolic status of Arabidopsis thaliana was crucial for the specific recruitment of Streptomycetaceae into the microbiota. Here, the Arabidopsis-Actinacidiphila interaction was further depicted by inoculating axenic Arabidopsis with Actinacidiphila cocklensis DSM 42063 or Actinacidiphila bryophytorum DSM 42138(previously named Streptomyces cocklensis and Streptomyces bryophytorum). We demonstrated that these two bacteria colonize A. thaliana wild-type plants, but their colonization efficiency was reduced in a chs5 mutant with defect in isoprenoid, phenylpropanoids and lipids synthesis. We observed that those bacteria affect the growth of the chs5 mutant but not of the wild-type plants. Using a mass spectrometry-based proteomic approach, we showed a modulation of the Arabidopsis proteome and in particular its components involved in photosynthesis or phytohormone homeostasis or perception by A. cocklensis and A. bryophytorum. This study unveils specific aspects of the Actinacidiphila-Arabidopsis interaction, which implies molecular processes impaired in the chs5 mutant and otherwise at play in the wild-type. More generally, this study highlights complex and distinct molecular interactions between Arabidopsis thaliana and bacteria belonging to the Actinacidiphila genus.
2024-01-29 | PXD041221 | Pride
Project description:Transcriptional profiling of an Fd-GOGAT1/GLU1 mutant in Arabidopsis thaliana
| PRJNA125189 | ENA
Project description:Photoperiod is a circannual signal measured by biological systems to align growth and reproduction with the seasons. To understand the effect of photoperiod of gene expression in Arabidopsis thaliana in the absence of exogenous sugar under constant light intensity, we performed time course mRNA-seq analysis on 13-day old seedlings across three photoperiods with triplicates to identify photoperiod-regulated genes.
2023-08-15 | GSE221846 | GEO