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Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS MBG 6108 ADVANCED LABORATORY TECHNIQUES IN GENOMICS ELECTIVE 3 0 0 12

Offered By

Molecular Biology and Genetics

Level of Course Unit

Third Cycle Programmes (Doctorate Degree)

Course Coordinator

ASSISTANT PROFESSOR YAVUZ OKTAY

Offered to

Molecular Biology and Genetics Molecular Biology and Genetics Biomedicine and Health Technologies

Course Objective

To have in-depth knowledge of laboratory methods and approaches used to analyze gene function and to develop skills for assessing the functional effects of mutations and variants.

Learning Outcomes of the Course Unit

1   to have a solid understanding of the essential methods used in genomics 2   to discuss the pros and cons of the in silico and wet-lab methods used to predict gene function 3   to discuss genome editing technologies 4   to be able to use CRISPR/Cas9 genome editing technology in cultured cells 5   To describe the methods used to interfere with gene expression 6   To explain the use of SILAC and 2D-DIGE methods in functional genomics applications 7   To be able to perform a literature search and present findings through oral and written means.

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description 1 The Present State and Future Direction of Integrated Genomic Analysis 2 NGS Technologies 3 Integrative Data-Mining Tools to Link Gene and Function 4 Determining the Effect of Mutations and DNA Methylation on Gene Function and Expression in Cancer Cells 5 A Method for Inducible Gene Over-Expression and Down-Regulation in Emerging Model Species 6 Construction and Application of Site-Specific Artificial Nucleases for Targeted Gene Editing 7 CRISPR/Cas9 Based Genome Editing 8 Applications of CRISPR/Cas9 in Basic and Translational Research 9 MIDTERM 10 Selection of Recombinant Antibodies from Antibody Gene Libraries 11 Construction of Simple and Efficient siRNA Validation Systems for Screening and Identification of Effective RNAi-Targeted Sequences from Mammalian Genes 12 Rapid Genetic Modification of Mouse Embryonic Stem Cells by Inducible Cassette Exchange Recombination 13 In Ovo Electroporation of miRNA-Based-Plasmids to Investigate Gene Function in the Developing Neural Tube 14 Proteomic Strategies: SILAC and 2D-DIGE Powerful Tool to Investigate Cellular Alterations 15 Assignment Presentations 16 Final Exam

Recomended or Required Reading

Textbook(s): Gene Function Analysis (Methods in Molecular Biology) 2nd edition, Springer, 2014 ISBN: 1627037209 Supplementary Book(s): Genomics: Essential Methods, Edited by Mike Starkey and Ramnath Elaswarapu, Wiley Press, 2010 ISBN: 9780470711576

Planned Learning Activities and Teaching Methods

Theoretical lecture with PowerPoint, literature review/discussion, and assignment presentations by students

Assessment Methods

SORTING NUMBER SHORT CODE LONG CODE FORMULA 1 ASG ASSIGNMENT 2 MTE MIDTERM EXAM 3 FIN FINAL EXAM 4 FCG FINAL COURSE GRADE ASG * 0.30 + MTE * 0.30 + FIN * 0.40 5 RST RESIT 6 FCGR FINAL COURSE GRADE (RESIT) ASG * 0.30 + MTE * 0.30 + RST * 0.40 *** Resit Exam is Not Administered in Institutions Where Resit is not Applicable.

Further Notes About Assessment Methods

None

Assessment Criteria

To be announced.

Language of Instruction

English

Course Policies and Rules

To be announced.

Contact Details for the Lecturer(s)

Yavuz.oktay@deu.edu.tr

Office Hours

To be announced.

Work Placement(s)

None

Workload Calculation

Activities Number Time (hours) Total Work Load (hours) Lectures 14 3 42 Preparations before/after weekly lectures 14 7 98 Preparation for midterm exam 1 28 28 Preparation for final exam 1 35 35 Preparing assignments 3 9 27 Preparing assignments 1 11 11 Preparing presentations 1 20 20 Project Preparation 1 30 30 Final 1 5 5 Midterm 1 5 5 TOTAL WORKLOAD (hours) 301

Contribution of Learning Outcomes to Programme Outcomes

PO/LO PO.1 PO.2 PO.3 PO.4 PO.5 PO.6 PO.7 PO.8 LO.1 5 LO.2 5 LO.3 5 LO.4 5 LO.5 5 LO.6 5 LO.7 5