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E-GEOD-40549

ABSTRACT: Spatial transcriptomes of iron-deficient and cadmium-stressed rice

OTHER RELATED OMICS DATASETS IN: PRJNA174253

TISSUE(S): Epidermis Plus Exodermis Of Root, Vascular Bundle Of Root, Vascular Bundle From New Leaf At The Lowest Node, Cortex Of Root, Vascular Bundle From Old Leaf At The Lowest Node

PROVIDER: E-GEOD-40549 | ExpressionAtlas | 2015-12-04

REPOSITORIES: ExpressionAtlas

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Dataset's files

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			Action	DRS
	E-GEOD-40549-analysis-methods.tsv	Tabular
	E-GEOD-40549-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-40549-configuration.xml	Xml
	E-GEOD-40549-percentile-ranks.tsv	Tabular
	E-GEOD-40549.condensed-sdrf.tsv	Tabular

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Project description:Spatial transcriptomes of iron-deficient and cadmium-stressed rice

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2018-11-12 | E-MTAB-7043 | biostudies-arrayexpress

Spatial transcriptomes of iron-deficient and cadmium-stressed rice

Project description:Several metals are essential nutrients for plants but metals are toxic in excess, deleteriously affecting crop yield and quality. Various kinds of genes involved in metal homeostasis have been investigated in detail over the past few decades and the mechanisms of how metals are absorbed from soil and distributed in plants have been elucidated. However, numerous genes related to metal homeostasis remain to be investigated and a comprehensive analysis of the expressions of these genes is required. In the present study, we investigated the spatial gene expression profile of iron (Fe)-deficient and cadmium (Cd)-stressed rice by a combination of laser capture microdissection and microarray analysis. We performed comprehensive microarray analysis of a rice root using laser microdissection and collected a total of 13 samples (3 replicates for each sample, 39 total microarray data). Roots of normal, Fe-deficient (-Fe) and Cd-stressed (+Cd) rice were separated into the vascular bundle (VB), cortex (Cor), and epidermis plus exodermis (EP). In addition, vascular bundles from new leaves (newDC) and old leaves (oldDC) at the lowest node, which are important for metal distribution, were separately analyzed.

2013-12-31 | E-GEOD-40549 | biostudies-arrayexpress

Transcriptome analyses of a C. glabrata strain deleted for the transcription factor Aft2.

Project description:In these experiments, we compared the transcriptomes of a wild type strain and an aft2 deleted strain of the pathogenic yeast Candida glabrata. The comparisons were performed in four different growth conditions: iron starvation (BPS treatment), selenite treatment, cadmium treatment and optimal growth conditions (YPD).

2018-11-12 | E-MTAB-7042 | biostudies-arrayexpress

Characterizing the role of rice NRAMP5 in Manganese, Iron and Cadmium Transport

Project description:OsNRAMP5 is involved in iron, manganese and cadmium transport. Goal was to determine the effects of knocking down OsNRAMP5 on global rice gene expression. Two experiments: Control condition experiment: root or shoot of WT vs. OsNRAMP5 RNAi plants. WT Cd treatment experiment: 4 weeks old WT plants grown under 0 or 10uM Cd for two weeks

2012-02-03 | E-GEOD-35502 | biostudies-arrayexpress

Spatial transcriptomes of iron-deficient and cadmium-stressed rice

2013-12-31 | GSE40549 | GEO

The effects of different chemical forms of iron fertilizer on cadium accumulation in dwarf Polish wheat are reflected in the differentially expressed genes

Project description:Purpose: To understand the effects of two different chemical forms of iron fertilizer on cadmium accumulation Methods:Cultivation and treatment for three weeks of dwarf Polish wheat seedlings by hydroponics, in triplicate, qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Iron fertilizer can effectively reduce cadmium concentration in plants Conclusions: Our study represents the different chemical forms of iron fertilizer have different mitigation effects on cadmium. The transcriptome gata showed that iron fertilizer have changed the cadimium metabolism

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Project description:Purpose: The goal of this study is to compare the different genetic mechanisms between Indica and Japonica rice under cadmium stress.

2023-01-02 | GSE196229 | GEO

Mouse Iron Distribution - Rich and Deficient iron diets (tracer)

Project description:Mouse Iron Distribution Dynamics Dynamic model of iron distribution in mice. This model attempts to fit the radioiron tracer data from Lopes et al. 2010 for mice fed iron deficient and rich diets by adjusting the rate of iron intake (vDiet) and the hepcidin synthesis rate (vhepcidin) independently for each experiment. All other parameters are those that provide the best fit for the adequate diet. This model includes the radioiron tracer species. Differences in parameter values between deficient, rich, and adequate diets: Diet vDiet vhepcidin Adequate 0.00377422 1.7393e-08 Deficient 0 8.54927e-09 Rich 0.00415624 2.30942e-08

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