Award details

Arabidopsis.info

Reference	BB/I001271/1
Principal Investigator / Supervisor	Professor Sean May
Co-Investigators / Co-Supervisors
Institution	University of Nottingham
Department	Sch of Biosciences
Funding type	Research
Value (£)	780,792
Status	Completed
Type	Research Grant
Start date	01/07/2010
End date	30/09/2013
Duration	39 months

Abstract

Arabidopsis.info at NASC is a resource that emerged consensually out of the community and which has continued for nearly 20 years based on hundreds of thousands of donated stocks and datasets from a vigorous worldwide Arabidopsis community. This centralisation of biological resources has proved crucial to the Arabidopsis community and has maximised access to these resources for researchers worldwide. We distribute nearly 100,000 stocks per annum globally. Our primary remit has therefore been to locate, capture and produce public genomic, mapping, array and germplasm data describing Arabidopsis and integrate them into a form that makes our data, array and seed services more accessible and useful to the Arabidopsis community. NASCarrays currently holds data from several thousand Arabidopsis Affymetrix Genechips. We have also provided a universally accessible version of Genespring workgroup for those Arabidopsis / plant community users who may not have local access to commercial analysis tools. All of the NASC services were developed centred around sample standardisation, data collection and curation, rapid data output, and open external dissemination. In this grant we will Incorporate ~100,000 additional stocks into the centre and distribute stocks at an increased level of demand (100,000 per annum). For array work we will take our GeneChip service into immediate full cost recovery including service contracts, analysis software and machine upgrades and bring array prices down by 40% for both Arabidopsis and Human chips. In parallel we will: Improve throughput to increase public data coverage for systems analysis; expand GeneChip species coverage (specifically targeting orphan crops, bioenergy and animal health for cheap diagnostics and trait discovery); Provide services for Tobacco, Brachypodium and Brassica GeneChips and; Develop a new Arabidopsis GeneChip (ATH2) with greatly superior gene coverage and other capabilities (from our cost recovery budget).

Summary

Impact Summary

The Nottingham Arabidopsis Stock Centre has a vital core role as infrastructure support for the highly distributed and prolific Arabidopsis community. Arabidopsis is the most widely used model system to study plant biology and has delivered numerous breakthroughs in understanding of plant and basic biological processes. Arabidopsis has underpinned the genomic revolution in plant science and represents the template on which other plant and crop genomes are annotated and assessed. Arabidopsis data is key to modern crop science and through that to food security and quality of life. Our services are equally available to Universities, institutes, companies and international users through simple, intuitive interfaces. Distribution abroad requires the same infrastructure as a purely UK resource but adds value by encouraging international donation of stocks, supplementing grant income and helping to consolidate the Arabidopsis and wider plant Community. All European plant research groups requiring Arabidopsis stocks are obliged to use NASC but thousands of non-Europeans access our resource. We provide materials, data and guidance worldwide (~100,000 seed tubes per year); and our existence helps tens of thousands of users to save time, money and effort through centralised services. For Affymetrix Genechips we have released over 4,000 public data files. Our ethos is entirely open access and in the years that we have been running we have redistributed all of our data many times over to the general community and to secondary providers such as ArrayExpress and GEO. We service not only Arabidopsis researchers but are broader as can be seen from the range of letters of support attached to this proposal. Computer scientists, biophysicists, crop scientists, and systems biologists use the data and materials that we distribute (plus our core audience of plant biologists). Our GeneChip services have been used directly by a very broad range of users including veterinary, bioenergy, medical and phylogenetics researchers in the UK and abroad. To demonstrate the breadth of our molecular users, a selected list of funders for recent UK work performed using our GeneChip service includes: DEFRA; Syngenta; SCRI, Warwick HRI; FERA (The food and environment research Agency; DFID (Department for International Development); The University of Nottingham; Horserace Betting Levy Board; NIAB (National Institute of Agricultural Botany); HGCA; LINK collaborative research; YARA; BBSRC; John Innes Centre; Rothamsted Research. Outside of the UK we have molecular users from the US to China and from Norway to South Africa. We have also been useful to BBSRC policy makers and marketing by our inclusion in BBSRC publications: the BBSRC Data Sharing Policy documentation held NASC up as one of four examples of good practice; the 2009 BBSRC Bioscience Resources for Food Security pamphlet specifically flagged us as a key collection seed resource and our transcriptome analysis service as supporting the UK Food Security priority. We provide multiple UK transcriptomic training sessions per year to our customers; to MRes and MSc/PhD students (both Nottingham and beyond); and to visitors. We have also performed workshops annually at the GARNet meeting; given many international talks and workshops - e.g. a lecture series in Hangzhou [China Partnership award 2008]; and the Chips, Crops & Computers Summer School, Hangzhou [RCUK award 2009]. Our outreach is extensive, regular and user-oriented. We also regularly publish primary research papers as ongoing technical development of our services, for dissemination and techniques accessibility. NASC has always hosted the community GARNish newsletter / GARNet website and acts as a repository for the MASC (Multinational Arabidopsis Steering committee) newsletter. We have ex-officio membership of MASC and its sub-committees ( Phenomics, Bioinformatics, multiparallel tools). NASC has also spoken at all GARNet meetings.

Committee	Research Committee C (Genes, development and STEM approaches to biology)
Research Topics	Crop Science, Plant Science, Technology and Methods Development
Research Priority	X – Research Priority information not available
Research Initiative	Bioinformatics and Biological Resources Fund (BBR) [2007-2015]
Funding Scheme	X – not Funded via a specific Funding Scheme

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