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 RNA and DNA by Bioanalyzer
- Affymetrix
- mRNA Sample Labeling
- Hybridization, Washing, Staining and Scanning
- Agilent
- mRNA and microRNA Sample Labeling
- Hybridization and Washing
- Scanning and Image Analysis
- Spotted Glass Arrays
- Manufacturing
- Scanning and Image Analysis
Equipment and procedures:
- 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.
- Agilent microarrays are supported with Agilent hybridization chambers and hybridization ovens, and a Perkin-Elmer Life Sciences ScanArray Express confocal laser scanner.
- A BioRad VersArray ChipWriter Pro is used for spotting pre-synthesized DNA onto glass slides. Hybridized chips are scanned with the Perkin-Elmer Life Sciences ScanArray Express scanner.
- 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 Broad Institute´s GenePattern, Affymetrix´s GeneChip Operating Software, TIGR´s Multi Experiment Viewer and Molecularware´s DigitalGENOME. Internally developed software includes SBEAMS, Addama, SLIMarray and Cytoscape, 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):
Litvak V, Ramsey SA, Rust AG, Zak DE, Kennedy KA, Lampano AE, Nykter M, Shmulevich I, Aderem A. (2009) Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals. Nature Immunology 10:437-43.
Hwang D, Lee IY, Yoo H, Gehlenborg N, Cho JH, Petritis B, Baxter D, Pitstick R, Young R, Spicer D, Price ND, Hohmann JG, Dearmond SJ, Carlson GA, Hood LE. (2009) A systems approach to prion disease. Molecular Systems Biology 5:252.
Wang K, Zhang S, Marzolf B, Troisch P, Brightman A, Hu Z, Hood LE, Galas DJ. (2009) Circulating microRNAs, potential biomarkers for drug-induced liver injury. PNAS 106:4402-7.
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