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Experiment: Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
Experiment Description
NASCArrays Experiment Reference Number: NASCARRAYS-76
Background:
Release of the caesium radioisotope 137Cs during weapons testing and industrial activity has contaminated thousands of hectares of agricultural land. Ingesting 137Cs has damaging and, sometimes, fatal effects. Most Cs enters the food chain through plants. The generation of _safe_ crops that exclude Cs and can be cultivated on contaminated land requires knowledge about the mechanisms for Cs uptake. Caesium is chemically similar to potassium (K) and might enter plants through K+ transporters in the plasma membrane of root cells.
To determine which transporters mediate Cs entry to plants, we have compared the accumulation of Cs and K by wildtype Arabidopsis with mutants lacking specific K+ transporters. Preliminary results showed that Cs concentration in the shoots of akt1-1, cngc1 and cngc4 (obtained from the Wisconsin T-DNA knockout facility) differed significantly from the Wassilewskija wildtype (Ws-2). A cursory investigation of their transcriptome, using the Affymetrix Arabidopsis 8K GeneChip, showed that the expression of several genes encoding K+ transporters differed between mutants and wildtype plants.
The aim of this GarNet project is to confirm the previous observations and to identify further genes that are differentially expressed in mutant and wildtype plants and which might impact on Cs accumulation.
Methods:
Arabidopsis mutants akt1-1 (N3762), cngc1 and cngc4 and their parental ecotype Wassilewskija -2 (N1601) will be sown on MS agar and transferred to hydroponics 21 days after germination. Seedlings will be grown for a further 7 days on full nutrient solution under continuous light in a Saxcil growth cabinet. RNA will be extracted from roots of mutant and parent (control) plants at the same growth stage and twelve complete-genome Affymetrix GeneChips (3 biological replicates of material from wildtype and 3 mutants) are requested to determine the differences in their transcriptome under comparable environmental conditions.
About the ExperimenterName: | Miss Corrina Hampton |
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Head of Lab Name: | Dr Philip White |
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Lab:
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Institute:
| Horticulture Research International |
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Address: | Horticulture Research International Wellesbourne Warwick
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Postcode:
| CV35 9EF |
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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: | 12 |
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| Experimental Parameters:
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parameter | genetic_modification |
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Quality Control Measures Taken:
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no-plants-pooled | 20-40 |
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References:
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| Other Information:
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ArrayExpress Accession | E-NASC-31 |
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Slides in this Experiment
Hybridisation Set: Hampton_genome_Rep1
Slide: Hampton_1-1_ws2_Rep1_ATH1 | | |
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Tissue:
| Whole roots |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
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Other Information:
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experimental_background | Wassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467. |
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Protocols for BioSource 1 |
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Slide: Hampton_1-2_akt1_Rep1_ATH1 | | |
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Tissue:
| Whole roots |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
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Other Information:
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experimental_background | Wassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467. |
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Protocols for BioSource 1 |
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Slide: Hampton_1-3_cngc4_Rep1_ATH1 | | |
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Tissue:
| Whole roots |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
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Other Information:
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experimental_background | Wassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467. |
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Protocols for BioSource 1 |
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Slide: Hampton_1-4_cngc1_Rep1_ATH1 | | |
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Tissue:
| Whole roots |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
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Other Information:
| |
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experimental_background | Wassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467. |
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Protocols for BioSource 1 |
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Hybridisation Set: Hampton_genome_Rep2
Slide: Hampton_1-5_ws2_Rep2_ATH1 | | |
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Tissue:
| Whole roots |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
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Other Information:
| |
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experimental_background | Wassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467. |
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Protocols for BioSource 1 |
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Slide: Hampton_1-6_akt1_Rep2_ATH1 | | |
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Tissue:
| Whole roots |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
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Other Information:
| |
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experimental_background | Wassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467. |
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Protocols for BioSource 1 |
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Slide: Hampton_1-7_cngc4_Rep2_ATH1 | | |
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Tissue:
| Whole roots |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
---|
Other Information:
| |
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experimental_background | Wassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467. |
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Protocols for BioSource 1 |
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Slide: Hampton_1-8_cngc1_Rep2_ATH1 | | |
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Tissue:
| Whole roots |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
---|
Other Information:
| |
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experimental_background | Wassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467. |
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Protocols for BioSource 1 |
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Hybridisation Set: Hampton_genome_Rep3
Slide: Hampton_1-9_ws2_Rep3_ATH1 | | |
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Tissue:
| Whole roots |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
---|
Other Information:
| |
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experimental_background | Wassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467. |
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Protocols for BioSource 1 |
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Slide: Hampton_1-10_akt1_Rep3_ATH1 | | |
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Tissue:
| Whole roots |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
---|
Other Information:
| |
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experimental_background | Wassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467. |
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Protocols for BioSource 1 |
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Slide: Hampton_1-11_cngc4_Rep3_ATH1 | | |
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Tissue:
| Whole roots |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
---|
Other Information:
| |
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experimental_background | Wassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467. |
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Protocols for BioSource 1 |
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Slide: Hampton_1-12_cngc1_Rep3_ATH1 | | |
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Tissue:
| Whole roots |
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Plant Ontology terms for this tissue type: | |
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| | | Unknown PO Term! | Diseased:
| Normal |
---|
Other Information:
| |
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experimental_background | Wassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467. |
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Protocols for BioSource 1 |
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Problems? Comments? Suggestions? Contact the Affymetrix Team