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The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis

Experiment Name: The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
Accession No. & GeneChip: AT18, ATH1-121501
Submitter: Experimenter: Dr Christian Dubos, submitted by Lishuang Shen
Experiment Type: effect of gene knock-out
organism part
Experiment Factor: genotype
organism part
Number of Replicates: 3
Quality Control Steps: biological replicates
Quality Control Description: None
Publication_id: None
Last Update Time: 2004-11-03 15:45:19
Expression Data
Access & Analysis:
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2. Browse Hybridizations and boxplots from experiment.

3. Visualization of hybridizations or treatment means with scatterplots and MvA plots.

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5. Create Gene List by filter probe sets for differentially-expressed genes.

6. Pattern Recognition on filtered gene list.
 
Description: This experiment submission 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 from NASCArray:
Experiment: The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
Submitted to this database: 2003-05-15

Experiment Description

Plants that exhibit secondary growth, such as trees, are a prominent feature of terrestrial ecosystems. Furthermore, secondary growth itself, particularly wood, has huge economic value. Despite the importance of secondary growth from both basic and applied science perspectives, little is known about the molecular mechanisms that underpin this facet of plant development. The proposed microarray experiments are designed to expand our knowledge of the regulation of secondary growth by combining the power of Arabidopsis genetics with complete transcriptome analysis. It is now well established that Arabidopsis can be grown under conditions that induce secondary growth in the hypocotyl, albeit small, wood.

We have grown 8500 Arabidopsis plants of different genotypes under these conditions and will extract RNA from the developing vascular cambia of these plants to subject them to complete transcriptome analysis.The mutants that we have chosen for these analyses are all related to each other on the basis of the fact that they impact dormancy in either seeds or shoots (abi1, aba1, max4, axr1, AtMYB61 knockout, AtMYB50 knockout). The mutants themselves are the core group of mutants that are the focus of a three laboratory consortium, funded under the BBSRC Exploiting Genomics Initiative, to investigate the molecular basis of meristem dormancy in Arabidopsis. The other partners in the consortium are Dr. Ottoline Leyser (York) and Dr. Michael Holdsworth (IACR). While the Leyser and Holdsworth groups have investigated the impact of these mutations on transcriptome activity in shoot meristems and seeds respectively, our work focuses on the vascular cambium. Thus, this work will not only provide insights into the regulation of cambial function, but, when compared with the existing datasets from the Leyser and Holdworth labs, the work should also provide insights into the relationship between dormancy-impacted phenomena in different meristematic regions. Beyond this, the specific work on the cambium-specific regulation of genes in the MYB61KO will provide even greater insights into the functioning of this important resource allocation regulator, as it will build on a significant complete transcriptome dataset that is already available through GARNet. In total, the proposed analyses will generate important new data that builds on existing datasets, to provide an even more comprehensive understanding of gene function, and genetic networks, in an important biological and applied context.

Please note that the sample numbers that we have provided below are meant to be the "base" number for each biological condition (mutant, etc.), and that there will be independent TRIPLICATE biological replicates produced for each condition. (ie. A-1 to A-12).


About the Experimenter
Name: Dr Christian Dubos
Head of Lab Name: Dr Malcolm Campbell
Lab:
Address: Department of Plant Sciences
University of Oxford
South Parks Rd
Oxford

Postcode: OX1 3RB
Country: UK
.
Telephone Number: +44 1865 275135
Fax Number: +44 1865 275037
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

About this Experiment
Experiment Type: ecotype_analysis; mutant; insertion_mutant; gene_knock_out; tissue_organ_specificity;
Experimental Parameters:
Quality Control Measures Taken:
no-plants-pooled 200-400/RNA sample



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.
Providers:
Name: Dr Christian Dubos
Institution: Department of Plant Sciences University of Oxford South Parks R
Head of Laborotary: Dr Malcolm Campbell
email:
Homepage:

 
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