SHUA13058U Introduction to recombinant DNA and Next Generation Sequencing techniques and applications
MSc Programme in Human Biology – elective course
MSc Programme in Molecular Biomedicine (joint with SCIENCE) – elective course
MSc Programme in Immunology and Inflammation – elective course
MSc Programme in Biomedical Engineering (joint with DTU) – elective course
MSc Programme in Quantitative Biology and Disease Modelling (joint with DTU) – elective course
Open for other MSc students in Natural Sciences or Health and Medical Sciences.
The fundamental principles of molecular cloning will be
explained with an emphasis on common applications in molecular and
cellular biology. The course will build on foundation principals
governing how DNA can be manipulated in a laboratory to generate
bespoke molecules for a wide range of purposes. Specific
applications of these concepts will cover
1. plasmid cloning, and the generation of transgenic mammalian cell
lines using CRISPR/Cas9 technologies
2. experimental workflows for NGS projects
3. analytical workflows for NGS projects
The course is designed with early stage researchers in mind and is
specifically structured to cover, and help alleviate, many of the
common pitfalls when working with recombinant DNA. The topics will
be covered in a lecture setting that will include group discussions
and workshop style interactions which will draw from participants
experiences.
After the course the student is expected to be able to:
Knowledge
- demonstrate a functional understanding of the latest approaches to molecular cloning and recombinant DNA technologies.
Skills
- apply this knowledge to a set of common experimental tools used in contemporary molecular biology and troubleshoot common experimental pitfalls.
- use various bioinformatic resources required for effective experimental design and use standard analysis pipelines for processing sequencing data.
- choose an appropriate plasmid cloning strategy for the desired purpose and implement it.
Competencies
- design and implement next generation sequencing projects for expression analysis and protein-DNA interaction analysis.
- critically evaluate the experimental design of published projects and understand the extent to which they may be prone to artefacts.
- V. Sgaramella and A. Bernardi. DNA Cloning, Encyclopedia of Genetics, 2001, Pages 544-550 2)
- Goodwin, S., McPherson, J. & McCombie, W. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17, 333–351 (2016). https://doi.org/10.1038/nrg.2016.493)
- Vieth, B., Parekh, S., Ziegenhain, C. et al. A systematic evaluation of single cell RNA-seq analysis pipelines. Nat Commun 10, 4667 (2019). https://doi.org/10.1038/s41467-019-12266-74)
- Lueken, M.D. and Theis, F.J. Current best practices in single-cell RNA-seq analysis: a tutorial. (2019). Current best practices in single-cell RNA-seq analysis: a tutorial., 15(6), e8746. http://doi.org/10.15252/msb.201887465)
- Adli, M. The CRISPR tool kit for genome editing and beyond. Nat Commun 9, 1911 (2018). https://doi.org/10.1038/s41467-018-04252-26)
- Aaron R. Quinlan, Ira M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, Volume 26, Issue 6, 15 March 2010, Pages 841–842, https://doi.org/10.1093/bioinformatics/btq0337)
- Love, M., Anders, S. and Huber W. Beginner’s guide to using the DESeq2 package. http://bioconductor.riken.jp/packages/2.14/bioc/vignettes/DESeq2/inst/doc/beginner.pdf8)
- Yamada T, Akimitsu N. Contributions of regulated transcription and mRNA decay to the dynamics of gene expression. Wiley Interdiscip Rev RNA. 2019;10(1):e1508. doi:10.1002/wrna.1508
Further course literature will be provided via Absalon course page.
- Category
- Hours
- Lectures
- 6
- Preparation
- 39
- Guidance
- 5
- Exam
- 20
- Total
- 70
Students will get individual oral feedback on their ideas for the topic of the final paper, and will then receive some written or oral feedback on the final written paper.
Open for credit transfer students and other external students.
Apply here:
Credit transfer students: https://healthsciences.ku.dk/education/for-students/credit-transfer-students/
Other external students: https://healthsciences.ku.dk/education/student-mobility/guest-students/
- Credit
- 2,5 ECTS
- Type of assessment
- Requirement to attend classesWritten assignment, 2 weeks
- Type of assessment details
- Written assessment
1) Students get an assignment and take it home. They should address a question from one of the lectures (choose one of three areas and agree on the question) and write an essay (10 pages), contributing their own critical assessment and using assigned recent research articles and reviews of the field. Assignment should be completed in one week and students upload the files by a deadline.
2) In-class written assessment, where students are expected to write a long answer to one of the questions on the topics of the lectures. There will be single question on every topic and questions will be distributed in advance, during the tutorials.
Essay and in-class written assessment will be evaluated according to the level of knowledge, skills and competencies, described in the learning outcome section, shown by student.
The 6 lessons will be followed by a project period of 2 weeks. (equivalent to 20 hours of work), where the participants will design an experiment they wish to persue for their own research interests, from the topics covered in the lectures, and submit it for evaluation with the course directors. The asignment is done individually, and a satifactory evaluation is needed to pass the course. During the project period, the participants will have the possibility of individual feedback/discussions with the course directors (by email). The course will be evaluated based on how well the student displayed an understanding of the course material, and how well that was applied to the chosen experimental setting. As this course is intended as an introduction to the topics, there should be clear evidence that students read more indepth about their chosen experiment approach, and this reading should be referenced in the final proposal. Self-directed reasearch should take up approcimately 75% of the allocated project workload (i.e. 15 hours) - Aid
- All aids allowed
- Marking scale
- passed/not passed
- Censorship form
- No external censorship
Internal examiners
Criteria for exam assesment
To achieve the grade Passed, the student must be able to:
Knowledge
- demonstrate a functional understanding of the latest approaches to molecular cloning and recombinant DNA technologies.
Skills
- apply this knowledge to a set of common experimental tools used in contemporary molecular biology and troubleshoot common experimental pitfalls.
- use various bioinformatic resources required for effective experimental design and use standard analysis pipelines for processing sequencing data.
- choose an appropriate plasmid cloning strategy for the desired purpose and implement it.
Course information
- Language
- English
- Course code
- SHUA13058U
- Credit
- 2,5 ECTS
- Level
- Full Degree Master
- Duration
- 1 block
- Placement
- Block 2
- Schedule
- A
- Course capacity
- 15 spots available for MSc students
Study board
- Study Board for Human Biology, Immunology and Neuroscience
Contracting department
- Center for Stem Cell Medicine (reNEW)
Contracting faculty
- Faculty of Health and Medical Sciences
Course Coordinators
- Jan Jakub Zylicz
(10-6f6673337f7e716e687f45787a736933707a336970)
Course responsible
Lecturers
Jan Zylicz, Associate Professor, Center for Stem Cell reNEW,
jan.zylicz@sund.ku.dk
Michaela Mrugala Rothová, Assistant Professor, Center for Stem Cell
reNEW, michaela.rothova@sund.ku.dk
Ana Rita Soares Monteiro, Postdoc, Center for Stem Cell reNEW,
rita.monteiro@sund.ku.dk
Molly Pleasants Lowndes, Postdoc, Center for Stem Cell reNEW,
molly.lowndes@sund.ku.dk
Jose Alejandro Herrera Romero, Postdoc, Center for Stem Cell reNEW,
iose.romero@sund.ku.dk