399673 Measurement techniques for bioinformatics (6 cr)

The course introduces students to the most fundamental molecular biology technologies including microarrays, mass spectrometry, SNP genotyping, in situ hybridization and cellular imaging. The course is particularly tailored for students with no previous molecular biology background.

News

15.6.2009	Results from 13 May exam are available.
28.5.2009	Summer re-exam for Biology for methodological scientists and Measurement techniques will be held on Tue 16 June 16.00-20.00 in Kumpula Exactum A111. Register to the exam with this form. Registration deadline is 9.6.2009. Note: you can only take courses where you registered to.
5.5.2009	Course exam will be held on 13 May at 9.00-11.30 in Biomedicum Lecture hall 3 (P-floor).
2.2.2009	First session the Module III: Mass Spectrometry is on 10 February at 9.15 in Biomedicum B401a.
7.1.2009	First session on Tuesday 13 January at 9.00 in Biomedicum room BP 20.
13.8.2008	Course web page is open.

The course consists tentatively of the following six modules.

How to work in the laboratory
Note: Each student has the change to extract their own DNA: for that purpose there will be nurses to take the blood samples in the beginning of the course. DNA will be used later on the course for genetical analysis. Giving the sample is voluntary, there will be some extra samples for those who do not like to give the blood sample.
Microarrays
Mass Spectrometry
Genotyping
In situ hybridization
Cellular Imaging

Schedule

The course is held in Spring 2009 in periods III and IV.

Sessions weekly on Tuesdays 9-12 and Wednesdays 9-16 (see schedule for exact times). Exceptions noted in the schedule.

Tue 13.1. 9-12 Module I: How to work in a laboratory (Biomedicum BP 20)
Wed 14.1. 9-16 Module I: How to work in a laboratory (Biomedicum BP 20)
Tue 20.1. Module II: Microarrays. 8:30-9:30 Introduction to Affymetrix GeneChip arrays (Rm B236a, 2nd floor). 9:30-17:00 Bioanalyzer analysis (Biochip Center, Rm BP16a, P-floor), reverse transcription, purification, IVT, labeling (Rm B223b, 2nd floor). [slides] (CS intranet)
Wed 21.1. Module II: Microarrays. 9:00-12:00 cRNA purification, fragmentation (Rm B223b, 2nd floor).
Tue 27.1. Module II: Microarrays. 15:00-16:30 Hybridization (Biochip Center, Rm BP16a, P-floor).
Wed 28.1. Module II: Microarrays. 8:30-12:00 Washing, scanning and assessment of data quality by GCOS software (Biochip Center, Rm BP16a, P-floor) .
Tue 3.2. Module II: Microarrays. 9:00-10:30 Basic Principles of Affymetrix data analysis (seminar room 8-9, P-floor) [slides]
Wed 4.2. No session
Tue 10.2. Module III: Mass Spectrometry. 9.15-12.00 (Biomedicum B401a)
Wed 11.2. No session
Tue 17.2. Module III: Mass Spectrometry. 9.15-12.00 (Biomedicum B401a)
Wed 18.2. No session
Tue 24.2. No session
Wed 25.2. No session
Tue 3.3. Module III: Mass Spectrometry. 9-12
Wed 4.3. No session
Tue 10.3. Module III: Mass Spectrometry. 9-12
Wed 11.3. Module IV: SNP Genotyping. 9.15-16.00 (BP20 Biomedicum)
Tue 17.3. Module IV: SNP Genotyping. 9.15-12.00 (BP20)
Wed 18.3. Module IV: SNP Genotyping. 9.15-12.00 (computer lab on P-floor)
Tue 24.3. No session
Wed 25.3. Module V: Cellular imaging. 9.00-16.00 (Meeting room 5-6 (B336)) [Schedule] [Course material] (CS intranet)
Tue 31.3. Module V: Cellular imaging. 9.00-12.00 (Meeting room 5-6)
Wed 1.4. Module V: Cellular imaging. 9.00-16.00 (Meeting room 4)
Tue 7.4. Module V: Cellular imaging. 9.00-12.00 (Meeting room 4)
Wed 8.4. Module V: Cellular imaging. 9.00-16.00 (Teamwork room 8-9)
Tue 14.4. No session
Wed 15.4. No session
Tue 21.4. Module VI: In situ hybridization. 9.00-12.00 [lecture slides 1] [lecture slides 2]
Wed 22.4. Module VI: In situ hybridization. 9.00-16.00
Tue 28.4. No session
Wed 29.4. No session
Tue 5.5. Module VI: In situ hybridization. 9.00-12.00
Wed 6.5. Module VI: In situ hybridization. 9.00-16.00
Tue 12.5. Module VI: In situ hybridization. 9.00-12.00
Wed 13.5. Exam. 9.00-11.30, Biomedicum Lecture Hall 3 (P-floor)

Enrolling for the course

You can register to the course here when the registration opens.

Maximum of 18 students will be taken to the course.

Grading

Course is graded on the scale 1-5. There will be an exam in the end of the course covering the six modules.

Summer exam

Summer re-exam for Biology for methodological scientists and Measurement techniques will be held on Tue 16 June 16.00-20.00 in Kumpula Exactum A111. Register to the exam with this form. Registration deadline is 9.6.2009. Note: you can only take courses where you registered to.

Contact

Course coordinator: Adjunct Professor Outi Monni (outi.monni@helsinki.fi)
Mass spectrometry module coordinator: Suvi Ravela (suvi.ravela@helsinki.fi)

Previous update: 15.06.2009 14:34 - Esa Pitkänen

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