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Gene expression and carbohydrate metabolism through the diurnal cycle | ||||
| Experiment Name: | Gene expression and carbohydrate metabolism through the diurnal cycle | |||
| Accession No. & GeneChip: | AT12, ATH1-121501 | |||
| Submitter: | Experimenter: Steve Smith, submitted by Lishuang Shen | |||
| Experiment Type: | time course | |||
| Experiment Factor: | time | |||
| Number of Replicates: | 2 | |||
| Quality Control Steps: | biological replicates | |||
| Quality Control Description: | None | |||
| Publication_id: | PMID: 15347792 Smith SM, Fulton DC, Chia T, Thorneycroft D, Chapple A, Dunstan H, Hylton C, Zeeman SC, Smith AM Diurnal changes in the transcriptome encoding enzymes of starch metabolism provide evidence for both transcriptional and posttranscriptional regulation of starch metabolism in Arabidopsis leaves. Plant Physiol. 2004 Sep;136(1):2687-99. Epub 2004 Sep 03. | |||
| Last Update Time: | 2004-06-10 09:36:47 | |||
| 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 Steve Smith Head of Lab Name: Dr Steve Smith Address: Institute of Cell and Molecular Biology University of Edinburgh The King_s Buildings Mayfield Road, Edinburgh Postcode: EH9 3JH Country: UK. Telephone Number: 0131 650 5318 Fax Number: 0131 650 5392 Experiment: This proposal is aimed at providing transcriptome data to underpin a long-term joint research programme of Steve Smith and Alison Smith. We are jointly studying starch synthesis and breakdown in Arabidopsis leaves, and individually studying other enzymes of carbohydrate metabolism (eg. sucrose synthases, invertases, sugar transporters). Collectively these enzymes are encoded by up to 100 known genes, but there are many others of relevance to our studies. For several years we have employed a defined set of growth conditions for this work (resulting in numerous publications). We have extensive data for changes in the amounts of starch, malto-oligosaccharides and sugars throughout the diurnal cycle in these plants, and we intend to quantitate numerous key enzymes. We now wish to profile changes in transcripts in these plants, so that this information can be correlated with changes in the amounts of key enzymes and metabolites. Analysis of the data sets will help us to relate the synthesis of certain enzymes to particular metabolic functions, and also to help identify genes encoding novel proteins involved in carbohydrate metabolism. Current research is aimed at discovering such novel proteins using proteomics approaches (BBSRC Grant: _Discovery and Functional Analysis of the Starch Proteome_). While the growth conditions (12h photoperiod, 150 umol/m2/s, 20C) and ecotype (Col-0) are specifically tailored to our experiments, they will be of value to the wider community, and could form the basis for collaborative studies with other groups. The experiment has involved sampling leaves at eleven different time points as follows: 0, 1, 2, 4, 8, 12, 13, 14, 16, 20, and 24 h (where time 0 is the onset of dark and 12 h is the onset of light). The 24 h time point is a repeat of 0 h. This sequence provides relatively more samples immediately after the light-dark transitions, when changes in metabolism are most pronounced. Plants were grown in a controlled environment chamber under defined conditions, and selected for harvest according to a random number generator. Three fully expanded leaves were harvested from each of 20 plants for each sample. Leaves were frozen at -80 C and a portion saved for metabolite and enzyme assays while RNA was isolated from the remainder. The RNA has been purified and is ready to send to Nottingham. | |||
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