Sean May
Click here for MS Powerpoint file
Abstract
NASC is currently a three stringed instrument, On the seed-side we provide seeds, DNA, phenomic information and ordering facilities. On the bioinformatics-side we provide a locally curated genome resource (AGR) with sequence, maps, and a variety of viewing and searching engines. The third string includes warehousing all of the other GARNet omics data as well as generating local data from transcriptomics experiments defined by the community.
We are providing two main facilities for transcriptomics:
- The first of these is a microarray synthesis, hybridisation and data-warehousing facility. This is fed by amplicons generated out of the CATMA consortium (please see talks from Jim Beynon and Martin Tricks groups) and will be taking in applications soon.
- A second, complimentary approach has been adopted to make hybridisations to oligonucleotide arrays available for the Arabidopsis community. This service is now accepting applications and we are currently in the process of purchasing and setting up the Affymetrix equipment at NASC.
In a separate talk (right), Jamie Kincaid from NASC will describe our bioinformatics services in more detail. In todays talk, as well as introducing the oligo service, I will be describing the reasons for the controls, standards and ontologies that Jamie will be detailing. This is intended as a general background for the transcriptomics applications that you will be submitting to the steering committee. Experimental design and controlled observations and vocabularies can be vital in order to ensure that your experiments are successful.
Jamie Kincaid: GARNet Microarray Bioinformatics
Click here for MS Powerpoint file
Abstract
Analysis of microarray data can be broadly divided into three categories.
- Primary analysis - quantifying spot intensities on the microarray slide, variation between replicate spots, standardization techniques.
- Secondary analysis - scatter plots, gene histories.
- Tertiary analysis - clustering groups of genes based on expression profiles using different clustering algorithms.
In order to facilitate all levels of analysis data from experiments will be stored in a way that adheres to current microarray standards and provides users with access to both raw and processed data.
This will be done by implementing the design proposed by the European Bioinformatics Institute for a microarray data repository - ArrayExpress; by adhering to standards proposed for describing and analysing microarray experiments; and by combining publicly available analysis tools with tools developed in house.
Data from GARNet proteomic and metabolomic projects will be incorporated in addition to the NASC stock catalogue and Arabidopsis Genome Resource database to allow researchers to approach the data from a number of different angles.
