Early Iron Deficiency Induced Changes in Arabidopsis Roots
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE15189 | GEO | 2009/03/13
SECONDARY ACCESSION(S): PRJNA116405
REPOSITORIES: GEO
Similar Datasets
Project description:Due to limited bio-availability of Fe, plants evolved adaptive alterations in development regulated at the transcriptional level. We investigated the early transcriptional response to Fe deficiency. A hydroponic system was used that allows bulk transferring of plantsand rapid Fe removal with little mechanical damage to the root systems.
2009-03-13 | E-GEOD-15189 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series:; GSE10496: Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe); GSE10497: Expression analysis of root developmental zones after iron deficiency (-Fe) treatment; GSE10501: Expression analysis of root cell-types after iron deficiency (-Fe) treatment; GSE10502: Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots Experiment Overall Design: Refer to individual Series
2008-06-11 | E-GEOD-10576 | biostudies-arrayexpress
Project description:Iron (Fe) deficiency is a yield-limiting factor for a variety of field crops across the world and generally results from the interaction of limited soil Fe bioavailability and susceptible genotype cultivation. Tomato, a Strategy I, model plant for Fe deficiency, is an important economical crop. Tomato responses in order to improve Fe uptake are based on acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells. Transcriptional profile obtained by roots (27-d) of 21-d-old tomato plants starved of iron for an additional week was compared with the transcriptional profile obtained for roots (27-d) of 21-d-old tomato plants grown for an additional week at 100 M-NM-<M Fe. Tomato plants were hydroponically grown in both cases. Three different biological replicates were used for each sample repeating the experiment three times. All samples were obtained pooling roots of six plants (27-d-old).
2012-03-22 | E-GEOD-31112 | biostudies-arrayexpress
Project description:Transcriptional profiling of rice genes analyzing the effect of knockdown of OsHRZ1 and OsHRZ2 in HRZ2i lines. NT and HRZ2i lines 1, 2 and 3 (2i-1, 2i-2 and 2i-3, respectively) were treated under iron sufficiency for 7 days (+Fe 7d) or under iron deficiency for 1 day (-Fe 1d) or 7 days (-Fe 7d) in hydroponic culture.
2013-10-17 | GSE39906 | GEO
Project description:In order to estimate the effects of protoplasting and FACS sorting procedures on -Fe regulated gene expression we generated expression profiles for whole roots that had been treated with -Fe for 24 hours and for roots that were protoplasted and FACS sorted after the initial 24 hour -Fe treatment. Little is known about how developmental cues affect the way cells interpret their environment. Here we characterize the transcriptional response of different cell layers and developmental stages of the Arabidopsis root to high salinity and find that transcriptional responses are highly constrained by developmental parameters. These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell-layers, several of which correspond to observable physiological changes. We show that known stress pathways primarily control semi-ubiquitous responses and use mutants that disrupt epidermal patterning to reveal cell-layer specific and inter-cell-layer effects. By performing a similar analysis using iron-deprivation we identify common cell-type specific stress responses and environment-independent biological functions that define each cell type. Experiment Overall Design: To estimate the effect that protoplasting and cell sorting has on the expression of -Fe regulated genes we prepared samples as in Birnbaum et al. (2005) Nat. Methods, except that all cells were collected after cell sorting. Cells were collected from roots that had been exposed to iron deficient (-Fe) conditions (0.3mM Ferrozine in MS media containing no ferrous sulfate) for 24 hours prior to protoplasting. Whole roots were also collected after a similar treatment regimen with -Fe. Three replicates were performed per condition.
2008-06-11 | E-GEOD-10496 | biostudies-arrayexpress
Project description:Iron (Fe) deficiency is a yield-limiting factor for a variety of field crops across the world and generally results from the interaction of limited soil Fe bioavailability and susceptible genotype cultivation. Tomato, a Strategy I, model plant for Fe deficiency, is an important economical crop. Tomato responses in order to improve Fe uptake are based on acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells.
2012-03-22 | GSE31112 | GEO
Project description:CsUBC13 was identified via proteomics from iron starvation treated Cucumber root. ubc13A is an ABRC seed stock (CS51269). CS851269 was purchased from ABRC and confirmed as homozygous Atubc13A knock-out T-DNA mutant. We generated transgenic arabidopsis with ectopic expression of CsUBC13 gene under control of the cauliflower 35S promotor. Both genotypes and Col-0 were used to investigate the transcriptional response to Iron (Fe) deficiency.
2009-07-07 | GSE16964 | GEO
Project description:Iron (Fe) and phosphorus (P) are essential nutrients with close geochemical association. They exist at low concentrations in surface waters and may be co-limiting resources for phytoplankton growth. However, the adaptive strategies of photosynthetic organisms to Fe/P co-limitation remain largely unknown. Here, we show that phosphorus deficiency increases the growth of Fe-limited cyanobacteria through a PhoB-mediated regulatory network. In addition to its well-recognized role in controlling phosphate homeostasis, PhoB regulates key metabolic processes crucial for Fe-limited cyanobacteria, including ROS detoxification and Fe uptake. Transcript abundances of PhoB-targeted genes are enriched in samples from the P-deplete ocean, and a conserved PhoB binding site is widely present in the promoters of the targets, suggesting that the strategy we discovered may be highly conserved. Our findings provide important molecular insights into the response of cyanobacteria to simultaneous Fe/P nutrient limitation and help in understanding how nutrient availability affects primary productivity in aquatic environments.
2024-03-06 | GSE260812 | GEO
Project description:Transcriptional profiling of rice genes analyzing the effect of knockdown of OsHRZ1 and OsHRZ2 in HRZ2i lines. NT and HRZ2i lines 1, 2 and 3 (2i-1, 2i-2 and 2i-3, respectively) were treated under iron sufficiency for 7 days (+Fe 7d) or under iron deficiency for 1 day (-Fe 1d) or 7 days (-Fe 7d) in hydroponic culture. Comparison between NT and HRZ2i lines at +Fe 7d, -Fe 1d and -Fe 7d. Biological replicates: 2-3 NT replicates, 3 HRZ2i replicates (one each for 2i-1, 2i-2 and 2i-3) for each treatment.
2013-10-17 | E-GEOD-39906 | biostudies-arrayexpress
Project description:We performed a time course analysis (TC data set) of the response of whole seedling roots to -Fe at 6 time points after transfer (3, 6, 12, 24, 48, and 72 hours). Little is known about how developmental cues affect the way cells interpret their environment. Here we characterize the transcriptional response of different cell layers and developmental stages of the Arabidopsis root to high salinity and find that transcriptional responses are highly constrained by developmental parameters. These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell-layers, several of which correspond to observable physiological changes. We show that known stress pathways primarily control semi-ubiquitous responses and use mutants that disrupt epidermal patterning to reveal cell-layer specific and inter-cell-layer effects. By performing a similar analysis using iron-deprivation we identify common cell-type specific stress responses and environment-independent biological functions that define each cell type. Keywords: time course analysis
2008-04-24 | GSE10502 | GEO