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Experiment: Treatment of Arabidopsis with low concn. of nitrate
Experiment Description
NASCArrays Experiment Reference Number: NASCARRAYS-479
The genomic response to low levels of nitrate was studied in Arabidopsis using the Affymetrix ATH1 chip containing more than 22,500 probe sets. Arabidopsis plants were grown hydroponically in sterile liquid culture on ammonium as the sole source of nitrogen for 10 d, then treated with 250 μm nitrate for 20 min. The response to nitrate was much stronger in roots (1,176 genes showing increased or decreased mRNA levels) than in shoots (183 responding genes). In addition to known nitrate-responsive genes (e.g. those encoding nitrate transporters, nitrate reductase, nitrite reductase, ferredoxin reductase, and enzymes in the pentose phosphate pathway), genes encoding novel metabolic and potential regulatory proteins were found. These genes encode enzymes in glycolysis (glucose-6-phosphate isomerase and phosphoglycerate mutase), in trehalose-6-P metabolism (trehalose-6-P synthase and trehalose-6-P phosphatase), in iron transport/metabolism (nicotianamine synthase), and in sulfate uptake/reduction. In many cases, only a few select genes out of several in small gene families were induced by nitrate. These results show that the effect of nitrate on gene expression is substantial (affecting almost 10% of the genes with detectable mRNA levels) yet selective and affects many genes involved in carbon and nutrient metabolism.
About the ExperimenterName: | Dr. Rongchen Wang |
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Head of Lab Name: | Professor Nigel Crawford |
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Lab:
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Address: | University of California, San Diego Division of Biological Sciences 9500 Gilman Drive, 0116 La Jolla, CA 92093-0116 USA
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Postcode:
| 92093-0116 |
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Country:
| USA |
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| Telephone Number:
| 18585342519 |
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Fax Number:
| 18585347108 |
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All of the data available in this website/database is free, and you
are free to do whatever you please with it. If you intend to publish
work based on any of this data, please acknowledge us, contact the
experimenter above, and either acknowledge them or use them as
co-authors in the work.
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| About this ExperimentExperiment Type:
| compound_treatment_design; |
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Number of Slides: | 8 |
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| Experimental Parameters:
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parameter | compound_based_treatment |
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Quality Control Measures Taken:
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References:
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Reference | Plant Physiol. 2003 June; 132(2): 556-567. |
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| Other Information:
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Slides in this Experiment
Hybridisation Set: Wang: Treatment of Arabidopsis with low concn. of nitrate_genome
Slide: Wang_1-1_WT-Col-250-micromolar-KCl-20-min-roots_Rep1_ATH1 | | |
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Tissue:
| Roots |
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Diseased:
| Control |
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in vivo Treatment:
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Treatment | 250 µM KCl |
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Additional Organism Information:
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Sample description | WT Col. 250 microM KCl 20 min, roots, replicate 1 |
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Other Information:
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Reference | Plant Physiol. 2003 June; 132(2): 556–567. |
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Protocols for BioSource 1 |
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Slide: Wang_1-2_WT-Col-250-micromolar-K-nitrate-20-min-roots_Rep1_ATH1 | | |
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Tissue:
| Roots |
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Diseased:
| Treatment |
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in vivo Treatment:
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Treatment | 250 µM KNO3 |
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Additional Organism Information:
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Sample description | WT Col. 250 microM KNO3 20 min, roots, replicate 1 |
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Other Information:
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Reference | Plant Physiol. 2003 June; 132(2): 556–567. |
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Protocols for BioSource 1 |
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Slide: Wang_1-3_WT-Col-250-micromolar-KCl-20-min-roots_Rep2_ATH1 | | |
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Tissue:
| Roots |
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Diseased:
| Control |
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in vivo Treatment:
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Treatment | 250 µM KCl |
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Additional Organism Information:
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Sample description | WT Col. 250 microM KCl 20 min, roots, replicate 2 |
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Other Information:
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Reference | Plant Physiol. 2003 June; 132(2): 556–567. |
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Protocols for BioSource 1 |
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Slide: Wang_1-4_WT-Col-250-micromolar-K-nitrate-20-min-roots_Rep2_ATH1 | | |
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Tissue:
| Roots |
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Diseased:
| Treatment |
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in vivo Treatment:
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Treatment | 250 µM KNO3 |
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Additional Organism Information:
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Sample description | WT Col. 250 microM KNO3 20 min, roots, replicate 2 |
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Other Information:
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Reference | Plant Physiol. 2003 June; 132(2): 556–567. |
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Protocols for BioSource 1 |
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Slide: Wang_1-5_Wild-type-Col-250-micromolar-KCL-20-min-shoots_Rep1_ATH1 | | |
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Tissue:
| shoots |
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Diseased:
| Control |
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in vivo Treatment:
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Treatment | 250 µM KCl |
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Additional Organism Information:
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Sample description | WT Col. 250 microM KCl 20 min, shoots, replicate 1 |
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Other Information:
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Reference | Plant Physiol. 2003 June; 132(2): 556–567. |
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Protocols for BioSource 1 |
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Slide: Wang_1-6_Wild-type-Col-250-micromolar-KNO3-20-min-shoots_Rep1_ATH1 | | |
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Tissue:
| shoots |
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Diseased:
| Treatment |
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in vivo Treatment:
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Treatment | 250 µM KNO3 |
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Additional Organism Information:
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Sample description | WT Col. 250 microM KNO3 20 min, shoots, replicate 1 |
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Other Information:
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Reference | Plant Physiol. 2003 June; 132(2): 556–567. |
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Protocols for BioSource 1 |
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Slide: Wang_1-7_Wild-type-Col-250-micromolar-KCL-20-min-shoots_Rep2_ATH1 | | |
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Tissue:
| shoots |
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Diseased:
| Control |
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in vivo Treatment:
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Treatment | 250 µM KCl |
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Additional Organism Information:
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Sample description | WT Col. 250 microM KCl 20 min, shoots, replicate 2 |
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Other Information:
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Reference | Plant Physiol. 2003 June; 132(2): 556–567. |
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Protocols for BioSource 1 |
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Slide: Wang_1-8_Wild-type-Col-250-micromolar-KNO3-20-min-shoots_Rep2_ATH1 | | |
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Tissue:
| shoots |
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Diseased:
| Treatment |
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in vivo Treatment:
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Treatment | 250 µM KNO3 |
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Additional Organism Information:
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Sample description | WT Col. 250 microM KNO3 20 min, shoots, replicate 2 |
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Other Information:
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Reference | Plant Physiol. 2003 June; 132(2): 556–567. |
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Protocols for BioSource 1 |
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Problems? Comments? Suggestions? Contact the Affymetrix Team