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Utrecht Genomics Center Microarray Facility

Utrecht Genomics Center Microarray Facility. Joop van Helvoort Dec, 8 th 2003. Frank Holstege Group. Utrecht Genomics Center (ABC/UMC). Wijmenga. Holstege. Bos. Burgering. etc. Microarray Facility. Bioinformatics. Transcription Regulation. Dik van Leenen Tony Miles

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Utrecht Genomics Center Microarray Facility

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  1. Utrecht Genomics CenterMicroarray Facility Joop van Helvoort Dec, 8th 2003

  2. Frank Holstege Group Utrecht Genomics Center (ABC/UMC) Wijmenga Holstege Bos Burgering etc. Microarray Facility Bioinformatics Transcription Regulation Dik van Leenen Tony Miles Marian Groot Koerkamp Joop van Helvoort 3.4 fte

  3. Microarray facility: tasks Microarray production Protocol development User support

  4. User support: philosophy Collaboration As many groups as possible Train users

  5. User support: steps • 1. Introductory discussions (1-2) • goals • experiment design • experimental issues • 2. Microarray course (1 week) • practical • performing a microarray experiment (wet lab) • image and data analysis (dry lab) • theory • 3. Access to: • arrays • lab space • equipment • software

  6. User support: arrays DNA preprocessing – ready to spot liquid handler

  7. User support: arrays spotter Collection from 384 well plate Deposition on glass surface 100 m 150 m

  8. User support: arrays spotted material: gene specific oligos (70-mer) or cDNAs oligos for the external controls: for various purposes (van de Peppel et al., 2003, EMBO reports, 4, p.387-393) suitable for two channel (Cy3 / Cy5) experiments; i.e. two sample comparison

  9. Human 1.1 array 20 000 spots 17 000 genes 3000 control spots

  10. S. cerevisiae array 16000 spots 6300 genes x2 3000 control spots

  11. Available Arrays spots genes+splice variants Human 1.1 20000 17000 Human 2.0 24500 21500 Yeast 16000 6300 (in duplo) Rat 12000 4500 (in duplo) coming soon: Mouse 35000 32000 Dog (cDNA) 23000 20000 (collaboration with Jan Mol and Rene van den Ham, Fac. Vet. Med.) All arrays contain 3000 control spots

  12. User support: lab space 4 benches available

  13. User support: equipment RNA/DNA quality and quantity assesment Bioanalyzer: integrity of RNA Total RNA • Spectrophotometer: quantity • cDNA synthesis (>30 µg total RNA) • RNA amplification (> 1 µg total RNA) (labeled) cDNA

  14. User support: equipment • Microarray experiment itself: • standard lab equipment • hybridisation: • manually for now • automated (future standard) (Ventana)

  15. User support: equipment • Image acquisition: • state-of-the-art scanner Scanner (Agilent)

  16. User support: equipment Workstations • Image analysis: transform tiff-image to data table • Imagene 5.6

  17. User support: equipment • Data quality check : • QQCC: QC etc. normalisation Raw data Normalized

  18. User support: equipment • Data storage and advanced analysis : • Genespring 6.0 / Genet + BASE:

  19. Financial Feasibility Costs: partial reimbursement Example: time course experiment: t = 0, 1, 2, 3, 4, 5 hours human samples, in duplo requires 10 microarrays Microarray Affimetrix Agilent Facility arrays 1250 8000 6000 experiment 400 / 800 1000 1000 support full no no costs in euros (for human: 1 microarray + 2 cDNA labeling + 1 hybridisation ~ 165 euro)

  20. Current state of affairs • Funding: • set up in 2000 with UMC financial support • and research grants Holstege • + ABC funding since Oct. 2002 • Users: • 29 users • 22 users within ABC

  21. Contact Contact www.genomics.med.uu.nl Joop van Helvoort Marian Groot Koerkamp j.vanhelvoort@med.uu.nl m.koerkamp@med.uu.nl Location: Stratenum

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