Initiated by Prof Mike Beale (Rothamsted Research) this projects original aim was to develop high throughput mass spectrometric methods for metabolite profiling in Arabidopsis. During the first three years under GARNet funding techniques and approaches were developed for screening of mutant or tagged lines of Arabidopsis and the progress of these projects can be viewed here.
The metabolite profiling service for the Arabidopsis has now moved to full cost recovery and is provided by the National Centre for Plant and Microbial Metabolomics at Rothamsted headed by Mike Beale and managed by Jane Ward.
The facilities available in the Centre consist of a modern suite of nuclear magnetic resonance (NMR) and mass spectroscopy (MS) laboratories, staffed by experienced spectroscopists, with access to extensive resources in analytical chemistry and growth of plants in controlled environment.
Services available to the Arabidopsis community include comprehensive analysis by NMR fingerprinting and also a range of targeted methods including analysis of flavonoids, carotenoids, fatty acids, amino acids and phenylpropanoids.
To find out more or apply for this service click here.
The GARNet proteomics service is provided by Paul Dupree and Kathryn Lilley at the Cambridge Centre for Proteomics (CCP). CCP was set up with BBSRC funding as part of investigating gene function initiative (IGF) to provide a proteomics resource for the UK Arabidopsis and Drosophila communities. The status and outcomes of GARNet supported projects are available here
Like other GARNet services CCP has now moved to full cost recovery and provides the Arabidopsis community with the following facilities.
- 1D and 2D gel electrophoresis
- Difference gel electrophoresis (DiGE - Cy dye labelling of proteins allowing running of two samples on the same 2D gel for direct quantitative comparison of protein expression)
- LC peptide separation
- MALDI-Tof mass spectrometry
- ESI-MS-MS mass spectrometry
To find out more or apply for this service go to
The NASC/GARNet Affymetrix service was set up to provide transcriptional profiling for the community. This service was so successful that by the end of 2003it had processed 900 chips and the Affymetrix data held at NASC constituted the largest collection of publicly accessible Affymetrix data for any organism worldwide.All the data produced by the NASC microarray service is available through the NASCArrays database and as a CD subscription service called AffyWatch.
The Affymetrix service at NASC has now moved to full cost recovery and provides users with the following:-
Pre-service advice and discussion.
Email acknowledgement receipt for RNA.
Total RNA Quality control
Nanodrop quantification check.
Agilent bioanalyser analysis
QC report & email confirmation to proceed.
cRNA Quality control & email confirmation to proceed if necessary.
Affymetrix chip & labelling costs.
Hybridisation & detection fluidics and materials.
Scan, QC and data tracking.
Data formatting (various)
CD including:
Raw data & Excel formatted data.
MIAME compliant auxiliary information.
Discussion of data interpretation by email or visit.
Six-month default confidentiality on plant data
Plant 'After Service' when confidentiality expires:
Free construction of XML/MAGE-ML and donation to ArrayExpress (EBI) according to the requirements for publication [in your name as experimenter].
Inclusion of your data into the NASCarrays database and integration into spot history, scatterplot and other on-line tools.
Integration of your data into PLANET [EU bioinformatics database] and associated links to other data resources.
Donation of data to TAIR.
If you wish to find out more or apply for this service click here.
The Gene Transfer Clone Identification and Distribution Service (GETCID) was initiated with GARNet funding by Ian Bancroft (JIC) to provide a library screening service for the Arabidopis community. From 2000-2002 it undertook 41 applications and conducted over 425 screens the details of which are available here. Since 2003 the service has moved to full cost recovery and is now available via the John Innes Genome Laboratory for further details and application for this service click here.
Previous Projects
In addition to the genomic services GARNet also funded the development of resources that would have long term value for the Arabidopsis community.
These include
Sequencing and tagging of transposon and insertion lines :
Projects initiated by Mike Bevan and Jonathan Jones have produced over 3500 unique tags which are available via NASC and searchable via AtiDB.
Sequence Tags for CATMA:-
GARNet funded Jim Beyon and his group(Warwick HRI) to sequencesmall sections of a subset of the 28,000 genes in Arabidopsis. This projected allowed
Warwick HRI, as part of GARNET, joined the CATMA (Complete Arabidopsis Thaliana Micro-Array) consortium. CATMA combined resources from the national programmes of several EU countries and resulted in the production of some 24,000 genome sequence tags (GSTs) from the Arabidopsis genome. Each GST was designed to be 150-500 bp in length and no more than 70% identical to any other Arabidopsis sequence. These are being used to produce microarrays around the EU and are available from NASC.
In silico analysis of GETCID Library:
In collaboration with Ian Bancroft(JIC),Martin Trick (JIC)produced a sequence indexed library of Arabidopsis transformable clones generated by the GETCID project that can be searched in silico rather than via hybridisation. This service is now available via AtiDB.
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