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Transcriptome analysis of glyoxylate cycle knock-out mutants in early stages of seedling development | ||||
| Experiment Name: | Transcriptome analysis of glyoxylate cycle knock-out mutants in early stages of seedling development | |||
| Accession No. & GeneChip: | AT11, ATH1-121501 | |||
| Submitter: | Experimenter: Johanna Cornah, submitted by Lishuang Shen | |||
| Experiment Type: | effect of gene knock-out | |||
| Experiment Factor: | genotype | |||
| Number of Replicates: | 3 | |||
| Quality Control Steps: | biological replicates | |||
| Quality Control Description: | None | |||
| Publication_id: | None | |||
| Last Update Time: | 2004-06-10 09:35:43 | |||
| Expression Data Access & Analysis: | Please select one action: 1. Batch download all data files at Download Center . 2. Browse Hybridizations and boxplots from experiment. 3. Visualization of hybridizations or treatment means with scatterplots and MvA plots. 4. Browse Samples from experiment. 5. Create Gene List by filter probe sets for differentially-expressed genes. 6. Pattern Recognition on filtered gene list. | |||
| Description: | This experiment is a courtesy of the Nottingham Arabidopsis Stock Centre's microarray database (http://ssbdjc2.nottingham.ac.uk/narrays/experimentbrowse.pl).The data was generated from NASC's Affymetrix service and offered for public access at BarleyBase. If you publish with this data, please reference data from NASC/GARNet: Craigon DJ., James N., Okyere J., Higgins J., Jotham J., May S. NASCArrays: A repository for Microarray Data generated by NASC's Transcriptomics Service. Nucleic Acids Research, (2004). volume 32, Database issue D575-D577. Following is the original experiment description: About the Experimenter Name: Dr Johanna Cornah Head of Lab Name: Dr Steven Smith Address: Institute of Cell and Molecular Biology University of Edinburgh King's Buildings Mayfield Road Edinburgh Postcode: EH9 3JR Country: UK Telephone Number: 0131 6505316 Fax Number: 0131 6505392 Experiment: Transcriptome analysis of glyoxylate cycle knock-out mutants in early stages of seedling development Experiment Description We aim to assess changes in gene expression in the early stages of seedling growth in glyoxylate cycle enzyme knock-outs. The analysis has two clear goals: firstly to discover those genes (and hence enzymes) whose expression changes markedly when a major switch in the pathway of seed lipid mobilisation is imposed, and secondly to use information from metabolome analysis in the same mutants, to discover the impact of well-defined changes in endogenous metabolites on the transcriptome.In wild type seedlings at approximately 2 days post-imbibiton, glyoxylate cycle activity reaches a peak associated with the mobilisation of lipid reserves for the growth of the developing seedling. We have isolated KOs in two enzymes unique to the glyoxylate cycle: malate synthase (ms) and isocitrate lyase (icl). The mutants have a visible seedling phenotype only in the absence of sugar and/or (high) light. Surprisingly, these mutants are able to mobilise their lipid reserves, apparently via a switch from glyoxylate cycle and gluconeogenesis to respiration (Eastmond et al. 2000, PNAS 97: 5669-5674). Transcriptomic analysis will allow us to establish what changes take place in expression of key genes involved in respiration and gluconeogenesis when the glyoxylate cycle is blocked in the KOs. This will in turn provide insights into the pathways of metabolism operating in these plants.In addition we are already in the process of having these mutants analysed by the GARNet metabolomics facility to quantitate changes in organic acids, amino acids and sugars. The use of the transcriptomics facility in parallel will allow us to determine how specific changes in metabolite levels affect the expression of genes involved in carbon and nitrogen metabolism, as well as in seedling development as a whole. One major strength of our approach is that both ms and icl mutants are blocked in the glyoxylate cycle and so will result in many common changes to the metabolome, but each may produce novel changes in specific metabolites which might allow correlation with specific changes in the transcriptome. The joint analysis of metabolome and transcriptome data will be carried out in collaboration with members of our School of Informatics.Whole seedlings will be grown in vitro and harvested 2 days after transfer of imbibed seed to continuous light, and used for RNA extraction. This corresponds to Principle Growth Stage 0.7 in the convention of Boyes et al. (Plant Cell 13; 1499-1510, 2001). Each mutant has a specific wild type control (Columbia in one case and Ws in the other) giving four RNA samples in total. 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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