E-GEOD-15189
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA116405
PROVIDER: E-GEOD-15189 | ExpressionAtlas | 2014-08-14
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-15189-analysis-methods.tsv | Tabular | |||
| E-GEOD-15189-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-15189-configuration.xml | Xml | |||
| E-GEOD-15189-percentile-ranks.tsv | Tabular | |||
| E-GEOD-15189.condensed-sdrf.tsv | Tabular |
Items per page: 5 1 - 5 of 78 |
Similar Datasets
Project description:Purpose: plants exposed to multiple simultaneous adverse growth conditions trigger molecular responses that differ from the sum of those to individual stressors. Copper and iron are fundamental elements required for proper photosynthesis, energy production, DNA metabolism and hormone sensing, among all. Therefore, copper and iron deprivation limits plant yield. In natural environments, simultaneous deficiency to copper and iron can occur. As part of a multiple high-throughput study to identify combinatorial responses to both copper and iron deficiency, proteomic profiling of Arabidopsis thaliana rosette leaves exposed to copper and/or iron deficiencies have been conducted.
2020-06-22 | PXD013598 | Pride
Project description:Deprivation of mineral nutrients causes significant retardation of plant growth. This slow growth is assumed to be associated with both nutrient specific transcriptional responses and additionally with common transcription patterns. In this study we adjusted the external supply of iron, potassium and sulfur to cause a similar retardation of growth. Global transcriptome analyses were performed to investigate whether the growth limitation by the different nutrient deficiencies triggered specific or similar transcriptional responses. The global transcriptome responded specifically to sulfur, iron or potassium deprivation. Arabidopsis thaliana plants were grown hydroponically under short-day conditions (8h light / 16h dark cycles) under full nutrient supply or under the limitation of sulfur, iron or potassium. Arabidopsis root material was harvested when the plants reached the age of 7 weeks (from sowing) and used for RNA extraction and hybridization on Affymetrix microarrays. Four biological replicates from each condition were analyzed.
2016-07-21 | E-GEOD-77602 | biostudies-arrayexpress
Project description:The budding yeast S. cerevisiae responds to depletion of iron in the environment by activating Aft1p, the major iron-dependent transcription factor, and by transcribing systems involved in the uptake of iron. Here we have studied the transcriptional response to iron deprivation, and have identified new Aft1p target genes. We find that other metabolic pathways are regulated by iron: biotin uptake and biosynthesis, nitrogen assimilation, and purine biosynthesis. Two enzymes active in these pathways, biotin synthase and glutamate synthase, require an iron-sulfur cluster for activity. Iron deprivation activates transcription of the biotin importer and simultaneously represses transcription of the entire biotin biosynthetic pathway. Multiple genes involved in nitrogen assimilation and amino acid metabolism are induced by iron deprivation, while glutamate synthase, a key enzyme in nitrogen assimilation, is repressed. A CGG palindrome within the promoter of glutamate synthase confers iron-regulated expression, suggesting control by a transcription factor of the binuclear zinc cluster family. We provide evidence that yeast subjected to iron deprivation undergo a transcriptional remodeling, resulting in a shift from iron-dependent to parallel, but iron-independent, metabolic pathways. A dose response design type examines the relationship between the size of the administered dose and the extent of the response of the organism(s). Using regression correlation
2006-02-07 | E-GEOD-4196 | biostudies-arrayexpress
Project description:The budding yeast S. cerevisiae responds to depletion of iron in the environment by activating Aft1p, the major iron-dependent transcription factor, and by transcribing systems involved in the uptake of iron. Here we have studied the transcriptional response to iron deprivation, and have identified new Aft1p target genes. We find that other metabolic pathways are regulated by iron: biotin uptake and biosynthesis, nitrogen assimilation, and purine biosynthesis. Two enzymes active in these pathways, biotin synthase and glutamate synthase, require an iron-sulfur cluster for activity. Iron deprivation activates transcription of the biotin importer and simultaneously represses transcription of the entire biotin biosynthetic pathway. Multiple genes involved in nitrogen assimilation and amino acid metabolism are induced by iron deprivation, while glutamate synthase, a key enzyme in nitrogen assimilation, is repressed. A CGG palindrome within the promoter of glutamate synthase confers iron-regulated expression, suggesting control by a transcription factor of the binuclear zinc cluster family. We provide evidence that yeast subjected to iron deprivation undergo a transcriptional remodeling, resulting in a shift from iron-dependent to parallel, but iron-independent, metabolic pathways. A dose response design type examines the relationship between the size of the administered dose and the extent of the response of the organism(s). Keywords: dose_response_design
2006-02-08 | GSE4196 | GEO
Project description:Exploring miRNA-related antisense transcription in Arabidopsis through RNA transcript profiling of smRNA pathway-defective mutants on a custom high-resolution oligonucleotide array.
2009-04-10 | GSE15199 | GEO
Project description:Transcription profiling by array of Arabidopsis protoplasted root cells after iron deprivation
2014-07-03 | E-GEOD-10496 | ExpressionAtlas
Project description:Transcription profiling by array of Arabidopsis mutant for nas4x after iron deprivation
2015-05-20 | E-GEOD-24348 | ExpressionAtlas
Project description:Deprivation of mineral nutrients causes significant retardation of plant growth. This slow growth is assumed to be associated with both nutrient specific transcriptional responses and additionally with common transcription patterns. In this study we adjusted the external supply of iron, potassium and sulfur to cause a similar retardation of growth. Global transcriptome analyses were performed to investigate whether the growth limitation by the different nutrient deficiencies triggered specific or similar transcriptional responses. The global transcriptome responded specifically to sulfur, iron or potassium deprivation.
2016-07-21 | GSE77602 | GEO
Project description:To dissect the mechanisms that control and mediate cellular iron homeostasis, we conducted quantitative high-resolution iTRAQ proteomics and microarray-based transcriptomic profiling of iron-deficient Arabidopsis thaliana plants. Proteomic and transcriptomic profiling of Arabidopsis Col and RING DOMAIN LIGASE1 (RGLG1) and RING DOMAIN LIGASE2 (RGLG2) double mutation in response to iron deficiency were conducted. This integrative analysis provides a detailed catalog of post-transcriptionally regulated proteins and allows the concept of a chiefly transcriptionally regulated iron deficiency response to be revisited.
2015-08-11 | PXD002126 | Pride
Project description:Purpose: plants exposed to multiple simultaneous adverse growth conditions trigger molecular responses that differ from the sum of those to individual stressors. Copper and iron are fundamental elements required for proper photosynthesis, energy production, DNA metabolism and hormone sensing, among all. Therefore, copper and iron deprivation limits plant yield. In natural environments, simultaneous deficiency to copper and iron can occur. As part of a multiple high-throughput study to identify combinatorial responses to both copper and iron deficiency, RNA-Seq profiling of Arabidopsis thaliana rosette leaves exposed to copper and/or iron deficiencies have been conducted. Methods: RNA-Seq libraries were prepared from total RNA of whole rosettes of 20-d-old plants treated for control conditions, copper deficiency, iron deficiency or simultaneous deficiency to both copper and iron for 10 d and sequenced using Illumina protocols. 2 independent plants were RNA-Seq-sequenced per treatment. Adaptor sequences were removed with Trimmomatic and the resulting reads mapped to the Arabidopsis genome (Araport11) with Tophat 2.1.1. Read counts and differential expression analysis were conducted with Cufflinks/Cuffdiff. Results: for RNA-Seq analysis a Tophat/Cuffdiff pipeline was designed. Each sample provided app. 9 million reads. After applying a cut-off of absolute log2(FC) ≥ 1 to controls and a FDR ≤ 0.05, copper deficiency led to 83 differentially expressed genes, followed by 1708 during iron deficiency, while the combinatorial treatment altered 2056 transcripts. Comparison of differential expressed genes among treatments indicated that double deficiency led to app. 45% rewiring of all detected transcriptional changes. Conclusions: our data support that combinatorial copper and iron deficiency treatments in plants triggers transcriptional responses that differ from those to single deficiencies.
2020-06-11 | GSE125894 | GEO