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GARNet

GARNet. Ottoline Leyser Karin van de Sande. The Plant Laboratory Department of Biology University of York. GARNet aims. To establish the infrastructure and expertise to provide reliable and efficient user driven functional genomics resources for the Arabidopsis community

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GARNet

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  1. GARNet Ottoline Leyser Karin van de Sande The Plant Laboratory Department of Biology University of York

  2. GARNet aims • To establish the infrastructure and expertise to provide reliable and efficient user driven functional genomics resources for the Arabidopsis community • To increase cohesion and collaboration in the UK Arabidopsis community

  3. Key Benefits • Service only • User driven • Wide range of services • High throughput • Fast public availability of data

  4. Transcript profiling Metabolite profiling Proteome profiling Forward and reverse genetic resources Bioinformatics Coordination GARNet components

  5. Sean May NASC Jim Beynon HRI Martin Trick JIC Affymetrix service 32 applications approved CATMA, Complete Arabidopsis Transcript MicroArray Joint European project, based on GSTs Transcript profiling

  6. Paul Dupree and Kathryn Lilley Cambridge Protein separation and identification service Open since March 2001 14 applications approved Proteome profiling

  7. Mike Beale IACR Metabolite separation and identification service Open since October 2000 19 projects approved Metabolite profiling

  8. Jonathan Jones JIC Ian Bancroft JIC High copy number transposon population Large insert gene transfer clone library screening service 31 projects approved Forward Genetics

  9. Mike Bevan and Jonathan Jones JIC Insertion site sequencing project Reverse Genetics

  10. Bioinformatics • Database to link information from all parts of project • Links to other Arabidopsis Functional Genomics projects world wide

  11. Co-ordination • Administration of the access to the resources • Web site with project news and application forms http://garnet.arabidopsis.org.uk • Annual conference Sept 17-18 2002

  12. Steering Committee • Prioritization of access to resources • Monitor progress on the project and report to BBSRC IGF board • Quality assurance • Bioinformatics interoperability

  13. GARNet website • http://garnet.arabidopsis.org.uk • General information • Service providers list • Steering committee list • Meeting registration form • Access to resources form • Prioritization of access information • Feedback form

  14. Access to GARNet • Application form • Prioritisation guidelines and system of ranking • http://garnet.arabidopsis.org.uk

  15. GARNet applications GARNet applications GeTCID Library Screening Service,  Ian Bancroft • 31 projects underway or completed • Gene involved in regulation of phenylpropanoid metabolism, B. Brown, Glasgow University. • Cloning of the AXR4 gene of Arabidopsis, A. Marchant, Nottingham University. • Study of NAC gene family in Arabidopsis, J.- L. Gallois, JIC. • Map-based cloning of a lesion-mimic, dwarf mutant of Arabidopsis (ldw1),Katell Jolivet, Imperial College at Wye. • Characterization of a STRUBBELIG homologue , David Chevalier, Kay Schneitz, University of Zurich . • Complementation of Arabidopsis leaf development mutation, Chan Man Ha, Hong Gil Nam, Pohang University, Korea .

  16. GARNet applications Metabolite analysis service,  Mike Beale • 19 projects underway • Hormone and phenylpropanoid analysis in a G protein alpha-subunit (GPA1) knock-out mutant of Arabidopsis, R. Hooley, IACR-Long Ashton. • Metabolic analysis of cellulose and lignin-deficient mutants in Arabidopsis, L. Jones, Manchester University. • The impact of ascorbate-deficiency on metabolism of Arabidopsis thaliana, N. Smirnoff, Exeter University. • RBZ function in nuclear / chloroplast targeting / signalling, H. Naested, Copenhagen University. • Salicylic and jasmonic acid concentrations in adr1 and a series of adr1 double mutant plants, G. Loake, Edinburgh University.

  17. GARNet applications Proteome analysis service,  Paul Dupree • 14 projects underway or completed • The response of a tolerant plant to water stress and proline as compared to Arabidopsis, Gaber Abodagallah, Paul Quick, University of Sheffield. • Expression profile and regulation of transport proteins in Arabidopsis tumours induced by Agrobacterium tumefaciens.Rosalia Deeken, Hedrich Rainer, University of Wurzburg. • Comparative analysis of the defence Proteome of Arabidopsis thaliana. Murray Grant, Imperial College at Wye. • Identification of nickel responsive proteins in the hyperaccumulator Alyssum lesbiacum. Robert Ingle, Andrew Smith, University of Oxford

  18. GARNet applications Transcriptome analysis service,  Sean May • 32 projects underway or completed • Transcriptional targets of DNA methylation, Ian Furner, University of Cambridge. • Modulation of leaf transcriptome by phytochromes and cryptochromes. Jorge Casal, University of Buenos Aires. • Transcriptomic analysis of the plastid protein import 1 (ppi1) and ppi3 mutants. Paul Jarvis, University of Leicester. • Changes in gene expression profiles under phosphate deficiency. John Hammond, Philip White. HRI Wellesbourne. • Functional Genomics of Ozone Stress in Arabidopsis. Eleri Short, Martin McAinsh, Lancaster University.

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