Events News Research CBS CBS Publications Bioinformatics
Staff Contact About Internal CBS CBS Other

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


O 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


O 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


O 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


O 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


O 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


O 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


O 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


O 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


O 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)


O Friday, June 18 - Friday, June 25


Analysis of your data and report writing
Reports are handed in Friday, June 25 at 14:00