Norwegian University of Science and Technology, Trondheim, Norway
| Aims | Programme | Registration | Accommodation | Course Website |
Background
The post-genomic challenge is to move from genomic sequence to a complete understanding
of gene function and biological processes. Microarray technologies offer one
of the key components in enabling an eventual 'Systems Biology' approach to
the gene function discovery process. It is through a better understanding of
the often fundamental and highly conserved biological pathways and regulatory
networks that we will be able to deal more efficiently with the care and prevention
of human defects and diseases.
Already, microarray technologies are widely implemented for gene function analysis,
making these technologies a powerful tool for gathering biological data, in
particular in the concept of 'Systems Biology'. This platform of technologies,
however, has still not fully matured and it may take additional time until platform
implementation, sample processing, experimental design and data extraction reach
a level of robustness that will allow full exploitation of its powers. Recent
scientific publications show, that microarray data produced under a series of
standardisation constraints has improved significance and sensitivity, when
assembled in data compendia. Thus, important aspects of technology maturation
can be achieved through a concerted effort towards benchmarking and standardisation.
Aims for the school/workshop
The proposed school/workshop fits in well with our continued efforts to further
develop standardization and experimental design as a foundation to improve the
quality of microarray data. We aim at bringing together European researchers
who have finished their masters degree and who want to learn and discuss microarray
gene expression analysis. There will be an emphasis on standardisation and benchmarking.
Concepts for the school/workshop
Five sessions are planned to cover central biological issues within microarray-based
transcript profiling, to provide an introduction to experimental design and
data analysis and to offer laboratory training in labelling and hybridization
as well as data storage and handling. The participants are also introduced to
the basics of microarray production and to developments of new microarray formats.
Venue:
Norwegian University of Science and Technology, Trondheim, Norway
23 - 27 May, 2005
The cost of accommodation at Elgeseter Hotel from 23 - 27th May (4 nights) will be covered by the course.
Programme:
Monday 23rd May:
09.45-10.15 Arrival and registration
10.15-10.25 Welcome Astrid Lægreid
Session I Microarray-based functional genomics
10.25-10.55 DNA microarray technology - principles and formats Ola Myklebost
11.00-11.45 Uncovering basic mechanisms in the molecular machinery of the cell
with microarray analysis Frank Holstege
11.50-12.35 Gene expression profiling of estrogen regulated genes Karin
Dahlman-Wright
12.35-13.15 Lunch
13.15-14.00 The predictive power of microarrays in the clinic - Speaker to be
confirmed
14.05-14.50 Microarray platform comparison: implications for multi-platform
data analysis Martin Kuiper
14.50-15.10 Coffee/Tea
15.10-15.55 Development
of new microarray formats Jörg Hoheisel
16.45-17.30 Discussion: Challenges in microarray-based functional genomics
Tuesday 24th May:
Session II Microarray in practice
08.30-09.15 Basic introduction into microarray production and analysis - potentials
and pitfalls Paul van Hummelen
09.20-10.00 Design and analysis of oligo-based arrays from Affymetrix Fiona
Brew
10.05-10.45 Analysis of printed arrays using the 3DNA labeling system - speaker
to be confirmed
10.45-11.00 Coffee/Tea
11.00-12.45 Laboratory part: Printed arrays Berit Doseth Eitrem
3DNA: cDNA synthesis Vidar Beisvåg and Hallgeir
Bergum
11.00-12.45 Laboratory
part: Affymetrix technology Svanhild Schønberg
3DNA: cDNA synthesis Caroline Hild Jakobsen and Javier Diaz
12.45-13.15 Lunch
13.15-14.15 Use of controls in microarrays
14.30-16.30 Laboratory
part: Printed arrays Berit Doseth Eitrem
Stop cDNA synthesis, neutralization of reaction mix, concentration of cDNA and
hybridization of cDNA to array Vidar Beisvåg and Hallgeir
Bergum
14.30-16.30 Laboratory
part: Affymetrix technology Svanhild Schønberg
cDNA cleanup, Start cRNA synthesis Caroline Hild Jakobsen and
Javier Diaz
Session III Presentation and discussion of research projects
17.00-18.30 Poster session Participants
19.30 Get together dinner
Wednesday 25th May:
Session II (cont'd) Microarray in practice
08.30-10.00 Laboratory part: Printed arrays Berit Doseth Eitrem
cDNA hybridization wash and dendrimer hybridization - Vidar Beisvåg
and Hallgeir Bergum
08.00-16.00 Laboratory part: Affymetrix technology Svanhild Schønberg
cRNA cleanup, quantitation, fragmentation, hybridization Caroline Hild
Jakobsen and Javier Diaz
10.15-11.15 Scanning and image analysis Heidi Lyng
13.00-16.00 Laboratory part: Printed arrays Berit Doseth Eitrem
Post 3DNA hybridization wash Vidar Beisvåg
Scanning and image analysis Hallgeir Bergum and Heidi Lyng
Session III (cont'd) Presentation and discussion of research projects
16.00-17.30 Presentation of microarray-based research projects at NMC Members
of the NMC
17.30-17.45 Coffee break
17.45-18.45 Microarray technology and genetic risk information - an ethical
perspective Berge Solberg
Thursday 26th May:
Session II (cont'd) Microarray in practice
08.30-10.00 Laboratory part: Printed arrays Berit Doseth Eitrem
Results from scanning Vidar Beisvåg and Hallgeir Bergum
08.30-15.00 Laboratory part: Affymetrix technology Svanhild Schønberg
Washing, staining and scanning and Results from scanning Caroline Hild
Jakobsen and Javier Diaz
10.00-10.15 Coffee break
Session IV Handling and storing microarray data
10.15-11.15 Introduction to BASE - BioArray Software Environment Johan
Vallon-Christersson
11.15-15.00 BASE: Hands on Hallgeir Bergum, Vidar Beisvåg,
Frode Jünge and Berit Doseth Eitrem
15.00-15.15 Coffee break
15.15-16.00 Storing microarray data in public repositories - Array Express and
MGED Helen Parkinson
16.00-16.35 Handling biological background information for microarray experiments:
the NMC Annotation database and eGOn Astrid Lægreid
16.40-17.25 Experimental design Ernst Wit
Friday 27th May:
Session V Microarray data analysis
08.30-09.30 Finding differentially expressed genes in microarray data Ernst
Wit
09.35-10.20 Normalization: Principles and solutions Anja von Heydebreck
10.20-10.35 Coffee break
10.35-11.20 Supervised and unsupervised analysis of microarray data Inge
Jonassen
11.25-12.10 Towards Systems Biology; combining data from different sources in
functional genomics data analysis Martin Kuiper
12.10-13.00 Lunch
13.00-13.30 Summary discussion and evaluation Astrid Lægreid
13.45-15.45 Exam
Registration is now closed.