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Experiment: Differential gene expression patterns in the phosphate deficient mutant, pho 1
Experiment Description
NASCArrays Experiment Reference Number: NASCARRAYS-102
Background:
The UK horticultural and agricultural industries routinely apply large amounts of inorganic fertiliser to maintain crop yield and quality, since chemical assays of soil nutrients are unreliable. Excessive fertiliser applications are costly and can lead to unnecessary pollution. A possible solution is to use sensor (GM or non-GM) technologies that exploit the changes in plant gene expression under incipient nutrient deficiency.
Aim:
The aim of this project is to use mutants with reduced leaf phosphate contents to identify genes upregulated in response to phosphate stress. Preliminary gene expression analysis has identified several phosphate responsive genes to be upregulated in the pho1 mutant. However, further replicates of the experiment are required to confirm these changes.
Methods:
Arabidopsis mutant pho1 (N8507) and its parent ecotype Columbia 2 (N907) will be grown on MS agar under identical conditions. RNA will be extracted from the rosette leaves of both parent and mutant and the same growth stage. By comparing the expression profiles, we will be able to differentiate between genes that are upregulated in leaves experiencing phosphate stress. Previously, two GeneChips have been used (mutant and parent) to provide preliminary data. A further two biological replicates are now required to confirm these results. Promoters and transcripts of these genes will underpin the development of novel sensor technologies, and knowledge of the gene expression profiles will improve our understanding of the physiology of plant mineral nutrition.
About the ExperimenterName: | Mr John Hammond |
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Head of Lab Name: | Prof Malcolm Bennett |
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Lab:
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Institute:
| University of Nottingham |
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Address: | Plant Sciences Division School of Biosciences University of Nottingham Sutton Bonington Campus Loughborough
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Postcode:
| LE12 5RD |
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Country:
| UK |
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| Telephone Number:
| 01789 470382 |
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Fax Number:
| 01789 470552 |
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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:
| genetic_modification_design |
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Number of Slides: | 6 |
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| Experimental Parameters:
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parameter | gene_knock_out |
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Quality Control Measures Taken:
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no-plants-pooled | 20 |
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References:
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| Other Information:
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Slides in this Experiment
Hybridisation Set: Hammond_genome_Exp2_RepSet1
Slide: Hammond_2-1_Col2wildtype_Rep1_ATH1 | | |
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Tissue:
| Rosette leaves |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
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Additional Organism Information:
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growth_conditions | Seeds were first washed in 70 % (v/v) ethanol/water, rinsed in distilled water and surface sterilised using 50 % (v/v) domestic bleach/water. Seeds were then rinsed three times in sterile distilled water and imbibed for 3-5 days at 4 degrees C to break dormancy. Seeds were grown in un-vented, polycarbonate culture boxes on 75 ml of 0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (Murashige and Skoog, 1962). Illumination was provided by a bank of 100W 84 cool fluorescent tubes (Philips, Eindhoven, Netherlands) giving an photon flux density between 400 and 700 nm of 50-80 µmol photons m-2 s-1 at plant height. Once plant reached the desired growth stage, rosette leaves were snap frozen in liquid nitrogen and total RNA extracted. |
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Other Information:
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experimental_background | Mutant: Pho1 (N8507). The identification of this mutant has previously been described by Poirier et al., (1991) Plant Physiol., 97, 1087-1093. The identification of the pho1 gene has recently been described by Hamburger et al., (2002) Plant Cell, 14, 889-902. |
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Protocols for BioSource 1 |
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Slide: Hammond_2-2_pho1mutant_Rep1_ATH1 | | |
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Tissue:
| Rosette leaves |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
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Additional Organism Information:
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growth_conditions | Seeds were first washed in 70 % (v/v) ethanol/water, rinsed in distilled water and surface sterilised using 50 % (v/v) domestic bleach/water. Seeds were then rinsed three times in sterile distilled water and imbibed for 3-5 days at 4 degrees C to break dormancy. Seeds were grown in un-vented, polycarbonate culture boxes on 75 ml of 0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (Murashige and Skoog, 1962). Illumination was provided by a bank of 100W 84 cool fluorescent tubes (Philips, Eindhoven, Netherlands) giving an photon flux density between 400 and 700 nm of 50-80 µmol photons m-2 s-1 at plant height. Once plant reached the desired growth stage, rosette leaves were snap frozen in liquid nitrogen and total RNA extracted. |
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Other Information:
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experimental_background | Mutant: Pho1 (N8507). The identification of this mutant has previously been described by Poirier et al., (1991) Plant Physiol., 97, 1087-1093. The identification of the pho1 gene has recently been described by Hamburger et al., (2002) Plant Cell, 14, 889-902. |
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Protocols for BioSource 1 |
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Hybridisation Set: Hammond_genome_Exp2_RepSet2
Slide: Hammond_2-3_Col2wildtype_Rep2_ATH1 | | |
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Tissue:
| Rosette leaves |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
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Additional Organism Information:
| |
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growth_conditions | Seeds were first washed in 70 % (v/v) ethanol/water, rinsed in distilled water and surface sterilised using 50 % (v/v) domestic bleach/water. Seeds were then rinsed three times in sterile distilled water and imbibed for 3-5 days at 4 degrees C to break dormancy. Seeds were grown in un-vented, polycarbonate culture boxes on 75 ml of 0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (Murashige and Skoog, 1962). Illumination was provided by a bank of 100W 84 cool fluorescent tubes (Philips, Eindhoven, Netherlands) giving an photon flux density between 400 and 700 nm of 50-80 µmol photons m-2 s-1 at plant height. Once plant reached the desired growth stage, rosette leaves were snap frozen in liquid nitrogen and total RNA extracted. |
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Other Information:
| |
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experimental_background | Mutant: Pho1 (N8507). The identification of this mutant has previously been described by Poirier et al., (1991) Plant Physiol., 97, 1087-1093. The identification of the pho1 gene has recently been described by Hamburger et al., (2002) Plant Cell, 14, 889-902. |
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Protocols for BioSource 1 |
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Slide: Hammond_2-4_pho1mutant_Rep2_ATH1 | | |
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Tissue:
| Rosette leaves |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
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Additional Organism Information:
| |
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growth_conditions | Seeds were first washed in 70 % (v/v) ethanol/water, rinsed in distilled water and surface sterilised using 50 % (v/v) domestic bleach/water. Seeds were then rinsed three times in sterile distilled water and imbibed for 3-5 days at 4 degrees C to break dormancy. Seeds were grown in un-vented, polycarbonate culture boxes on 75 ml of 0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (Murashige and Skoog, 1962). Illumination was provided by a bank of 100W 84 cool fluorescent tubes (Philips, Eindhoven, Netherlands) giving an photon flux density between 400 and 700 nm of 50-80 µmol photons m-2 s-1 at plant height. Once plant reached the desired growth stage, rosette leaves were snap frozen in liquid nitrogen and total RNA extracted. |
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Other Information:
| |
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experimental_background | Mutant: Pho1 (N8507). The identification of this mutant has previously been described by Poirier et al., (1991) Plant Physiol., 97, 1087-1093. The identification of the pho1 gene has recently been described by Hamburger et al., (2002) Plant Cell, 14, 889-902. |
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Protocols for BioSource 1 |
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Hybridisation Set: Hammond_genome_Exp2_RepSet3
Slide: Hammond_2-5_Col2wildtype_Rep3_ATH1 | | |
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Tissue:
| Rosette leaves |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
---|
Additional Organism Information:
| |
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growth_conditions | Seeds were first washed in 70 % (v/v) ethanol/water, rinsed in distilled water and surface sterilised using 50 % (v/v) domestic bleach/water. Seeds were then rinsed three times in sterile distilled water and imbibed for 3-5 days at 4 degrees C to break dormancy. Seeds were grown in un-vented, polycarbonate culture boxes on 75 ml of 0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (Murashige and Skoog, 1962). Illumination was provided by a bank of 100W 84 cool fluorescent tubes (Philips, Eindhoven, Netherlands) giving an photon flux density between 400 and 700 nm of 50-80 µmol photons m-2 s-1 at plant height. Once plant reached the desired growth stage, rosette leaves were snap frozen in liquid nitrogen and total RNA extracted. |
---|
Other Information:
| |
---|
experimental_background | Mutant: Pho1 (N8507). The identification of this mutant has previously been described by Poirier et al., (1991) Plant Physiol., 97, 1087-1093. The identification of the pho1 gene has recently been described by Hamburger et al., (2002) Plant Cell, 14, 889-902. |
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Protocols for BioSource 1 |
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Slide: Hammond_2-6_pho1mutant_Rep3_ATH1 | | |
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Tissue:
| Rosette leaves |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
---|
Additional Organism Information:
| |
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growth_conditions | Seeds were first washed in 70 % (v/v) ethanol/water, rinsed in distilled water and surface sterilised using 50 % (v/v) domestic bleach/water. Seeds were then rinsed three times in sterile distilled water and imbibed for 3-5 days at 4 degrees C to break dormancy. Seeds were grown in un-vented, polycarbonate culture boxes on 75 ml of 0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (Murashige and Skoog, 1962). Illumination was provided by a bank of 100W 84 cool fluorescent tubes (Philips, Eindhoven, Netherlands) giving an photon flux density between 400 and 700 nm of 50-80 µmol photons m-2 s-1 at plant height. Once plant reached the desired growth stage, rosette leaves were snap frozen in liquid nitrogen and total RNA extracted. |
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Other Information:
| |
---|
experimental_background | Mutant: Pho1 (N8507). The identification of this mutant has previously been described by Poirier et al., (1991) Plant Physiol., 97, 1087-1093. The identification of the pho1 gene has recently been described by Hamburger et al., (2002) Plant Cell, 14, 889-902. |
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Protocols for BioSource 1 |
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Problems? Comments? Suggestions? Contact the Affymetrix Team