The Arabidopsis Functional Genomics Network

AtGenExpress at databases:

Developmental samples
Stress treatments
GARNET: Light treatments, Pathogen infection, Base line experiments


Overview

  1. General information: Grant proposal (new proposal), Project: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana (A project coordinated by Detlef Weigel, Thomas Altmann and Lutz Nover)
  2. Principal investigator for AFGN: Prof. Dr. Lutz Nover, Botanisches Institut, Molekulare Zellbiologie, FB Biologie und Informatik der J. W. Goethe Universität Frankfurt; Biozentrum N200 3OG, Marie-Curie-Strasse 9, 60439 Frankfurt am Main, nover@cellbiology.uni-frankfurt.de
  3. Summary
    The Affymetrix technology for expression profiling with the ATH1 full genome chip allows the reliable detection of about 24,000 protein-coding genes of Arabidopsis. It includes the RNA processing and labelling technology and the Gene Array Scanner with workstation and data processing software. Altogether this represents a unique combination of tools broadly used worldwide. Based on this technology, the AFGN groups propose an international cooperation project (AtGenExpress) to generate a gene expression profiling database covering about 230 data sets derived from 500 RNA samples with financial support by the DFG. This part includes samples for Arabidopsis development, stress responses, light response and pathogen interaction. It will be complemented by 80 data sets from the NSF 2010 project (USA) on pathogen responses, by 170 data sets from RIKEN (Japan) on hormone responses and by about 50 data sets from the MPIs in Tübingen and Golm. The overall data base derived from more than 1300 microarrays, i.e. more than 30 million data points, will be released to the public as part of the international Gene Expression Omnibus (GEO) and ArraExpress data bases. Data processing and publication will be mannaged by the NSF-supported Arabidopsis database (TAIR, USA).
    AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana
    Coordinated by Detlef Weigel(1), Thomas Altmann(2), and Lutz Nover(3)
    (1) Department of Molecular Biology, MPI for Developmental Biology, Spemannstrasse 37-39, D-72076 Tübingen
    (2) Institut für Biochemie und Biologie, Universität Potsdam, c/o MPI für molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Golm
    (3) Molekulare Zellbiologie, Biozentrum, Goethe Universität Frankfurt, Marie-Curie-Str. 09, D-60439 Frankfurt
  4. Executive Summary
    In the 1990s, the genomes of several multicellular eukaryotic model organisms were sequenced, including those of the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and the crucifer Arabidopsis thaliana. However, DNA sequencing can only be considered as the first step in understanding the function of these genomes. The Arabidopsis community has been at the forefront of initiating concerted actions toward functional genomics. For example, the ambitious goal of creating knock out lines for every Arabidopsis gene has almost been reached through the generation of sequence-defined T-DNA and transposon lines. Arabidopsis is also the only organism among the three aforementioned where already considerable information on natural allelic and genetic diversity exists, and it is the only species, apart from humans, where genome-wide linkage disequilibrium has been measured.
    In contrast to the genome sequencing of Arabidopsis with significant contributions from Germany and other European countries, there was so far no major technological impact on the functional genomics phase. Here, we propose a large-scale service project for genome-wide expression profiling in Arabidopsis (AtGenExpress) designed and coordinated by the German Arabidopsis Functional Genomics Network (AFGN), but incorporating strong elements of international cooperation. To our knowledge, no other comparable initiative exists. Its completion and public presentation depends on the strong support by the DFG, but it requires very substantial contributions by RIKEN (Japan), NSF (USA; via funding of TAIR and the 2010 program) , BBSRC (UK; via funding of the GARNET initiative), and the Max-Planck-Society.
    The expression profiles will be determined using the Affymetrix ATH1 gene chip for analysis of the Arabidopsis thaliana wild type (var. Col-0). The created data sets will not only serve as the main reference to the Arabidopsis transcriptome, but will serve as the principal information resource for data mining by Arabidopsis researchers worldwide. This will create an unprecedented opportunity for the establishment of new hypotheses and thus will aid researchers to rationalize detailed studies. Most notably, the functional genomics analyses conducted in the AFGN and 2010 projects will strongly benefit by providing the tools to specifically design studies with mutants created by T-DNA insertions or RNAi knock-out. Finally, AtGenExpress will be an indispensable reference database also for research with other plants, in particular with crop plants for which only microarrays with a limited set of gene-specific probes are available.
    We propose to generate a sufficiently comprehensive gene expression profile covering about 230 data sets from Arabidopsis development, stress responses, light response and pathogen interaction (Tables 1-3) complemented by the above mentioned contributions of about 290 data sets each 20 from the MPIs in Tübingen (D. Weigel) and Golm (M. Stitt), 80 from the NSF 2010 project (pathogen responses) and 170 from RIKEN (hormone responses). The overall database represents an open system encouraging the addition of further, more specific data sets. Thus, it will continue to grow in its usefulness.
    The AtGenExpress project sensu stricto has three phases (for a time schedule see 7.):
    1. Selected expert groups will generate RNA samples in triplicate or duplicate from the plant material defined in Tables 1-3.
    2. To achieve jointly the necessary throughput, three sites (MPI Tübingen, RZPD Berlin, and the GARNET microarray facility at Nottingham) will be used for the processing of the RNA and generation of the expression data with Affymetrix ATH1 arrays. All have long experience in Affymetrix technology and data handling and apply the same standardized procedures.
    3. All data will be released as soon as possible to the Gene Expression Omnibus (GEO) database of NCBI. Data for each gene will be displayed on the NSF-supported Arabidopsis database (TAIR). At this stage, a web server will be set up that will allow data mining of researchers from all over the world. In addition, work stations with the Affymetrix software at different places in Germany (Tübingen, Potsdam, Halle, Frankfurt) will provide the means for data mining by AFGN co-workers.

Coordinator: Lutz Nover, Detlef Weigel and Thomas Altmann