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Gene expression and carbohydrate metabolism through the diurnal cycle
Steve Smith, Institute of Cell and Molecular Biology, University of Edinburgh
Experiment design (22 hybridizations)
•0hr •1hr •2hr •4hr •8hr •12hr •13hr •14hr •16hr •20hr •24hr

This experiment is a courtesy of the Nottingham Arabidopsis Stock Centre's microarray database ([complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

Experiment Name: Gene expression and carbohydrate metabolism through the diurnal cycle
Accession No: AT12
Microarray: ATH1-121501
Visibility: public
Experiment Type:
Experiment Factor(s):
•0hr  •1hr  •2hr  •4hr  •8hr  •12hr  •13hr  •14hr  •16hr  •20hr  •24hr
Quality Control: biological replicates
Treatment summary:
 time  # replicates
 0hr  2
 1hr  2
 2hr  2
 4hr  2
 8hr  2
 12hr  2
 13hr  2
 14hr  2
 16hr  2
 20hr  2
 24hr  2
Total hybridizations: 22
Description: This experiment is a courtesy of the Nottingham Arabidopsis Stock Centre's microarray database ( 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.
Publication: none
Created: 2004-06-10 09:36:47
Last Update: 2008-08-05 10:58:08
Submitter: Lishuang Shen
Name: Steve Smith
Institution: Institute of Cell and Molecular Biology, University of Edinburgh
Head of Laboratory: Dr Steve Smith

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