Introduction to recombinant DNA and Next Generation Sequencing techniques and applications

Course content

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.

Education

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.

Learning outcome

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.

Lectures and Individual assignments.

- 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.

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.

A completed Bachelor degree within the Biomedical and Natural Sciences. Strong background in molecular biology, cell biology and genetics is required.

The course and assessment are in English. Students must be able to understand, speak, read and write scientific English at a high level.

Individual
Feedback by final exam (In addition to the grade)

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.

ECTS
2,5 ECTS
Type of assessment
Course participation
Written assignment, 2 weeks
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 assessment

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.

Single subject courses (day)

  • Category
  • Hours
  • Lectures
  • 6
  • Preparation
  • 39
  • Guidance
  • 5
  • Exam
  • 20
  • English
  • 70