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Course Programme 2004
The course will be held from June 7 - 25, 2004 (incl.)
Please note that due to the limited space, only those registered can participate
in the course.
Lectures and exercises will take place at the Center for Biological Sequence Analysis at
the Technical University of Denmark,
building 208, room 007, in Lyngby.
Daily schedule:
The course will start at 9 am and end no later than 17 pm,
Lunch from 12 - 13
 Monday, June 7
- 9.00-10:30
- Introduction to the course and a general overview:
Gene expression and DNA microarray technology (Lecture slides)
-
- 10:30-11.00
- In the lab:
- Demonstration of microarray facilities at CBS
- 11.00-11.30
- Experimental design
(Lecture slides)
-
- 11.30-12.00
- Sample preparation
(Lecture slides)
-
- 12.00-13.00
- Lunch Break
- 13.00-14.00
- OligoWiz - Probe design
(Lecture slides)
-
- 14.00-14.15
- Coffee Break
- 14.15-16.00
- Probe design
Nielsen et al., 2003
OligoWiz
Regular expressions
Tuesday, June 8
- 9.00-12.00
- In the lab:
Sample preparation
Check the quality/quantity of the RNA
(Protocol)
-
- 12.00-13.00
- Lunch Break
- 13.00-17.00
- In the lab:
Sample preparation
Group 1 - 2: - Import Probes into Geniome One
- Overnight synthesis of array #1
Wednesday, June 9
- 9.00-12:00
- In the lab:
- Sample preparation
- 12.00-13.00
- Lunch Break
- 13.00-17:00
- In the lab:
- Sample preparation
- Demonstration of Affymetrix equipment
Group 3 - 4: - Import Probes into Geniome One
- Overnight synthesis of array #2
Thursday, June 10
- 9.00-12:00
- In the lab:
- Sample preparation
- 12.00-13.00
- Lunch Break
- 13.00-17:00
- In the lab:
- Sample preparation
Group 5 - 6: - Import Probes into Geniome One
- Overnight synthesis of array #3
Friday, June 11
- 9.00-12:00
- In the lab:
- Sample preparation
- 12.00-13.00
- Lunch Break
- 13:00-13:00
- Hybridization, scanning and image analysis
(Lecture slides)
- 13:45-14:00
- Coffee Break
- 14:00-15:00
- Normalization and statistical analysis
(Lecture slides)
Analysis of data: Clustering, PCA and classification
(Lecture slides)
- 15:00-15:15
- Coffee Break
- 15:15-16:30
- GenePublisher exercise
Cook book
Monday, June 14
- 9.00-11:15
- In the lab:
- Sample preparation
- 11:15-12:00
- Case story: Arabidopsis thaliana
- 12.00-13.00
- Lunch Break
- 13:00-13:45
- Case stories:
Bacillus subtilis
(Lecture slides)
Listeria monocytogenes (Lecture slides)
- 13:45-14:00
- Coffee Break
- 14:00-14:30
- Case story: Adjuvants in vaccines
- 14:30-17:00
- In the lab:
- Sample preparation
Tuesday, June 15
- 9.00-12:00
- In the lab:
- Sample preparation
- 12.00-13.00
- Lunch Break
- 13.00-17.00
- In the lab:
- Group 1 - 2: Overnight hybridization #1
- Group 3 - 4: Overnight hybridization #2
Wednesday, June 16
- 9.00-12.00
- In the lab:
- Group 1 - 2: Detection #1
- Group 3 - 4: Detection #2
- 12.00-13.00
- Lunch Break
- 13.00-17.00
- In the lab:
- Group 5 - 6: Overnight hybridization #3
Thursday, June 17
- 9.00-12.00
- In the lab:
- Group 5 - 6: Detection #3
- 12.00-13.00
- Lunch Break
- 13.00-14.15
- Analysis of generated data (groups of 4)
GenePublisher
- 14.15-14.30
- Coffee Break
- 14.30-16.00
- Normalization and statistical analysis
(scatter plots of normalized data)
Friday, June 18 - Friday, June 25
Analysis of your data and report writing
Reports are handed in Friday, June 25 at 14:00
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