MEB707 - METHODS IN GENOME ANALYSIS

Course Name Code Semester Theory
(hours/week)		 Application
(hours/week)		 Credit ECTS
METHODS IN GENOME ANALYSIS MEB707 2nd Semester 3 2 4 10
PrequisitesLimited to a quota of 5 students
Course languageTurkish
Course typeMust 
Mode of DeliveryFace-to-Face 
Learning and teaching strategiesLecture
Discussion
Demonstration
Experiment
 
Instructor (s)Prof. Çetin KOCAEFE, Prof. Didem DAYANGAÇ-ERDEN 
Course objectiveThe aim of this course is to teach laboratory methods about genomics and functional investigations of genes and nucleic acid fragments.  
Learning outcomes
  1. Students will; Knows the various aims, methodology and pitfalls of PCR applications. Can define the principal framework of primer design and employ PCR techniques according to the scientific question.
  2. Knows principles and limitations of RFLP and DNA sequence analysis methods which are used in order to analyze PCR products.
  3. Employs cloning techniques for in-vivo amplification.
  4. Gains information about the application principles of Real Time PCR technique, becomes capable of answering questions related the principles of probe design and quantitative expression profiling.
  5. Knows the fundemental principles of protein analysis techniques.
  6. Gains the ability to choose the appropriate technique to solve a problem in the field of genomics.
  7. Interpretes and discusses scientific data.
Course ContentIn this course; in vivo and in vitro cloning methods, gene expression analysis at the RNA and protein level, high throughput technologies and their application areas will be discussed.  
References1. Molecular Cloning: A laboratory manual. Ed. Michael R. Green, Joseph Sambrook. CSHL Press.
2. Real time PCR Ed. T. Dorak. Taylor & Francis.
3. Current Protocols in Molecular Biology, Wiley Interscience. 

Course outline weekly

WeeksTopics
Week 1The use of genomics tools and application principles in the diagnosis of inherited disorders and identification of the molecular basis of disease.
Week 2Amplification of DNA-I: Polymerase Chain Reaction (PCR), principles and practical applications (Laboratory)
Week 3Amplification of DNA-II: Analysis of PCR products (Laboratory) a. Electrophoretic techniques. b. Fragment analysis (RFLP) c. Sequence analysis
Week 4Nucleic acid hybridization techniques: Blotting, probe preparation and labeling approaches, applications of hybridization methods
Week 5Cell based cloning methods-I: Plasmid vectors; cloning and gene expression vectors, gene transfer techniques
Week 6Cell based cloning methods-II: (Laboratory) a. Plasmid transformation b. Colony picking and expansion c. Plasmid isolation and analysis
Week 7Laboratory
Week 8Mammalian gene transfer: Viral and non-viral vector systems and fundamentals of gene replacement therapy
Week 9Gene expression analysis-I: Northern Blot, semi-quantitative RT-PCR and quantitative real-time PCR methods and fields of application
Week 10Gene expression analysis-II (Laboratory) a. RNA isolation b. cDNA synthesis c. Real-time PCR
Week 11Protein analysis-I: Protein analysis methods in functional genomics (western blotting, immunostaining, elisa)
Week 12Protein analysis-II: (Laboratory) a. Western blotting b. Immunostaining
Week 13Laboratory
Week 14Applications of high-throughput genomics technologies: Parallel sequencing and microarray systems (gene expression analysis and SNP analysis)
Week 15Preparation for the final exam
Week 16Final exam

Assesment methods

Course activitiesNumberPercentage
Attendance00
Laboratory740
Application00
Field activities00
Specific practical training00
Assignments00
Presentation00
Project00
Seminar00
Midterms00
Final exam160
Total100
Percentage of semester activities contributing grade succes740
Percentage of final exam contributing grade succes160
Total100

WORKLOAD AND ECTS CALCULATION

Activities Number Duration (hour) Total Work Load
Course Duration (x14) 14 3 42
Laboratory 7 15 105
Application000
Specific practical training000
Field activities000
Study Hours Out of Class (Preliminary work, reinforcement, ect)149126
Presentation / Seminar Preparation000
Project000
Homework assignment000
Midterms (Study duration)000
Final Exam (Study duration) 11515
Total Workload3642288

Matrix Of The Course Learning Outcomes Versus Program Outcomes

D.9. Key Learning OutcomesContrubition level*
12345
1. Learn and process the information in the field of cell biology at an academic level (KNOWLEDGE).     
2. Learn and process the information in the field of molecular biology and genetics at an academic level (KNOWLEDGE).     
3. Learn and process the information in the field of inheritance at an academic level (KNOWLEDGE).     
4. Learn and process the information in the field of genomics and functional genomics at an academic level (KNOWLEDGE).   X 
5. Have theoretical/ practical skills for preparing and carrying out an independent research project (SKILLS).     
6. Follow and discuss national/international publications (SKILLS).      
7. Apply ethical and legal rules at the institutional, national and international level (SKILLS).     
8. Design and implement studies efficiently related to genomics technologies (SKILLS).    X
9. Use information technologies and bioinformatics tools effectively (SKILLS).    X
10. Take responsibility in a team and/or carry out independent research (QUALIFICATION).     
11. Gain critical thinking and solve scientific problems in accordance with ethical reflection (QUALIFICATION).     
12. Prepare scientific publications for national/international-refereed journals (QUALIFICATION).     
13. Apply biosafety rules and follow good laboratory practices (QUALIFICATION).    X
14. Have competence in setting up a new laboratory infrastructure in the field of genomics and manage a working team (QUALIFICATION).    X
15. Make scientific presentations at the national/international meetings (QUALIFICATION).     

*1 Lowest, 2 Low, 3 Average, 4 High, 5 Highest