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

2. Frank Holstege Group Microarray Facility BioinformaticsTranscription Regulation Dik van Leenen Tony Miles Marian Groot Koerkamp Joop van Helvoort Utrecht Genomics Center (ABC/UMC) WijmengaHolstegeBosBurgeringetc. 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 100  m 150  m Collection from 384 well plate Deposition on glass surface spotter

8. 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 User support: arrays

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. spotsgenes+splice variants Human 1.1 2000017000 Human 2.0 24500 21500 Yeast 160006300 (in duplo) Rat 12000 4500 (in duplo) coming soon: Mouse 3500032000 Dog (cDNA) 2300020000 (collaboration with Jan Mol and Rene van den Ham, Fac. Vet. Med.) All arrays contain 3000 control spots Available Arrays

12. User support: lab space 4 benches available

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

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

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

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

17. User support: equipment Data quality check : QQCC: QC NormalizedRaw data normalisation etc.

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

19. Financial Feasibility Example: time course experiment: t = 0, 1, 2, 3, 4, 5 hours human samples, in duplo requires 10 microarrays MicroarrayAffimetrixAgilent Facility arrays125080006000 experiment400 / 80010001000 supportfullnono costs in euros Costs: partial reimbursement ( 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 www.genomics.med.uu.nl Joop van HelvoortMarian Groot Koerkamp j.vanhelvoort@med.uu.nl m.koerkamp@med.uu.nl Location: Stratenum