The Microarray Facility exists to serve the research community at the Institute for Systems Biology by generating high-quality microarray data from experimental samples in a high-throughput, timely manner. Support is provided to investigators during processing of samples and analysis of data. In addition, the Microarray Facility disseminates information about new methods developed internally or externally, and supports investigators as they use these new methods.
Services offered:
- Quality Assessment of Total RNA, cRNA and Fragmented cRNA
- RNA Labeling for Affymetrix chips
- Hybridization, Washing, Staining and Scanning of Affymetrix chips
- Manufacture of Spotted Glass Arrays
- Scanning of Glass Arrays
- Spotfinding of Glass Arrays
- ChIP-Chip sample processing
Equipment and procedures:
The Microarray Facility uses a BioRad VersArray ChipWriter Pro for spotting pre-synthesized DNA onto glass slides. For small experimental runs, we employ an internally developed ink-jet in situ array synthesizer. Hybridized chips are scanned with a Perkin-Elmer Life Sciences ScanArray 5000 confocal laser scanner.
The Microarray Facility uses the latest Affymetrix instruments available, including the Fluidics Station 450, Hybridization Oven 640 and GeneChip Scanner 3000 with Autoloader and High-Resolution Upgrade. Sample quality is checked at three stages of processing using an Agilent 2100 Bioanalyzer.
A blend of externally and internally developed software is used for image analysis and quality assurance, as well as data management, analysis and storage. External software packages used include Molecularware´s DigitalGENOME, Affymetrix´s GeneChip Operating Software and TIGR´s Multi Experiment Viewer. Internal software includes the SBEAMS database, Cytoscape network visualization and intergration tool, as well as numerous smaller pieces of software.
Example(s) of projects that use the services of the facility:
- Identifying gene expression markers in Type 1 diabetes that will allow early diagnosis and prognosis of disease.
- Discovery of the molecular mechanisms of Prion disease through expression profiling
Representative publication(s):
Gilchrist M, Thorsson V, Li B, Rust AG, Korb M, Kennedy K, Hai T, Bolouri H, Aderem A. (2006) Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 441:173-8.
Kaur A, Pan M, Meislin M, Facciotti MT, El-Gewely R, Baliga NS. (2006) A systems view of haloarchaeal strategies to withstand stress from transition metals. Genome Research 16:841-54.
Smith JJ, Sydorskyy Y, Marelli M, Hwang D, Bolouri H, Rachubinski RA, Aitchison JD. (2006) Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism. Molecular Systems Biology 2:2006.0009.
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Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:286.
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