Utrecht Genomics Center Microarray Facility

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 genessplice 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 (gt30
µg total RNA) RNA amplification (gt 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
Normalized
Raw data
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_at_med.uu.nl
m.koerkamp_at_med.uu.nl
Location Stratenum