|
|
 |
|
|
|
|
Return to Projects page
Functional Genomic Technologies
Workpackages
- WP 1-1 Expression Maps
- WP 1-2 Experimental Systems
- WP 1-3 Bioinformatics
Coordinators: Nick Hastie (1-2, 1-3), Gregor Eichele (1-1)
Partners: Duncan Davidson, Jamie Davies, Andreas Schedl,
Olivier Devuyst, Pierre Courtoy, André Brändli, Seppo Vainio, Thomas Willnow, Matthias Kretzler,
Erik I. Christensen
Specific objectives in Functional genomics technologies (Topic 1)
- develop neew methods for high throughput in situ
gene expression analysis
- develop renal organ cultures to study gene function by knockdown and gain-of-function approaches
- establish databases/repositories for tools, methodologies, and results of functional genome studies
- develop kidney atlas for spatio-temporal description of mechanisms of renal development/disease
Methods for automated high throughput in situ hybridization (ISH) on kidney
sections and optical projection tomography (OPT) will be used to establish
a three-dimensional (3D) map of the embryonic and the adult kidney transcriptome
in mouse and Xenopus. Techniques
for knockdown (siRNA) and gain of function studies (viral gene
transfer) will be adapted to renal organ cultures to develop new experimental
systems to systematically study gene function. All data produced in the various
EuReGene projects will be incorporated in specific databases.
WP 1-1 Expression Maps (Partners 2a, 5, 6, 11, 12, 14)
Specific objectives: We aim to establish
global 3D gene expression maps of the embryonic and the adult kidney by combining
techniques of automated high-throughput ISH on histological sections with
3D image reconstruction using optical
projection tomography (OPT). Partners 2a and 11 in this consortium
have pioneered both techniques.
Specific tasks:
- Task 1-1-1 High-throughput in situ hybridization
- Task 1-1-2 OPT microscopy
WP 1-2 Experimental systems (Partners 2a, 3a, 12)
Specific objectives: our goal is to adapt
the renal organ culture as a tool for studying genes through
knockdown and gain-of-function studies. This proposal draws on
our recent success in showing
that siRNA works effectively in embryonic kidney rudiments.
The ultimate aim is to develop high thoughput multiplex approaches
that enable functional analysis of large numbers of genes. An
important tool for this will be mice that express GFP reporters
in specific compartments within the developing kidney.
Specific tasks:
- Task 1-2-1 Renal organ cultures
- Task 1-2-2 reporter mouse lines
WP 1-3 Bioinformatics (Partners 1, 2a, 6, 16)
Specific objectives: Bioinformatics is an
indespensible tool to integrate and synergize the wide spectrum of approachess to understanding gene function. WP 1-3 will provide public
access to all data arising from the diverse EuReGene projects. It will integrate available information from our and from other sources into the spatio-temporal
framework of a kidney atlas where novel relationships can be uncovered in an environment that is not constrained by current concepts.
Specific tasks:
- Task 1-3-1 Establishment of data standards
- Task 1-3-2 Establishment of databases
- Task 1-3-3 Establishement of a kidney atlas
- Task 1-3-3 Extension of the kidney atlas
|
|
|
|
|
|
