Practicum Experimental Genomics
6 EC
Semester 1, period 2
50521PAG6Y
Genomics technologies, like (single cell) Next Generation Sequencing (NGS), are rapidly developing and are being used extensively within life sciences. For instance, mRNA sequencing is used to study differences in gene expression in populations of cells that have undergone experimental treatments or to determine which genes play a role in diseases such as cancer. The power of these techniques lies in the fact that they allow for genome wide expression analysis. Or to put it differently, to study all expressed genes in a population of cells at once. These types of analyses are termed transcriptomics and involves a series of steps, starting at experimental design and ending in data analysis and interpretation. It is important that the students gain experience with these techniques while understanding both the advantages and limitations.
In this busy and full-time course, students will perform two gene expression (Q-RT-PCR) experiments on P19 cells, and work with their own mRNA sequencing dataset. P19 cells are stem cells, derived from an intriguing form of cancer termed teratocarcinoma. They have the capacity to respond to signaling molecules and can differentiate into all cell types of the body, including neurons and beating heart muscle. The students will design and execute their own experiments and gain experience with all steps involved in transcriptomics. The basics of the practical work are widely applicable but the focus will this year be on differentiation towards neurons. In addition to practical work and data analysis, a journal club, guest speakers and masterclasses will give a broad overview of genomics techniques and applications, ranging from Q-RT-PCR to single cell RNA sequencing techniques. In the final week, the focus will be on single cell techniques and students will learn how to understand and explain complex techniques. The ultimate goal is that students are capable of understanding when and how to use genomics technologies in novel contexts.
Will be made available during the course, via the canvas web site
Not applicable
Labcoat (long sleeves)
Lab(note)book
MS Office, PDF reader, Internet browser (Firefox, Chrome, Safari,..)
Lectures: On the first day an introductory lecture will be given, for which participation is highly recommended. During the course various lectures on the basics and applications of next gene sequencing in ongoing research projects are offered.
Working groups: During the practical, various complex techniques will be applied. Prior to the day a specific technique is performed at the wet lab, a deeper understanding of its operation and protocols is sought through working groups. The preparation for the working groups is scheduled as a self-study. The aim is to jointly arrive at the protocol that will be carried out in the wet lab. The subject matter discussed during these working groups is exam material.
Practical: On the basis of the preliminary discussions and the techniques and protocols discussed during the working groups, the experiments in the lab are performed in pairs, with assistance available. The results of the tests must be recorded individually by the students in a lab journal.
Computer practical: Students are prepared for a basic analysis of the data and analyze the data independently as much as possible, but with supervision.
Self-study: The preparation of the working groups takes place by means of self-study. Time has been set aside for this.
Excursion: Students will visit the SILS sequencing facility (MAD) and learn about the hardware that is required for NGS experiments
Report Writing: A short scientific report will be written with emphasis on placing data in the appropriate context and generating new hypotheses based on gene expression analysis
|
Activiteit |
Uren |
|
Hoorcollege |
17 |
|
Practicum |
48 |
|
Werkgroep |
14 |
|
Zelfstudie |
25 |
|
Toets |
3 |
|
Write report |
15 |
Programme's requirements concerning attendance (OER-B):
Additional requirements for this course:
Attendance at practicals and working groups is compulsory. Attendance at the introductory lectures is strongly recommended, because if you don't attend, you won't know what to do during the practical. Attendance at other lectures is strongly recommended too since there is no written documention that you could study instead.
You may miss a maximum of two days of (computer) practicals and/or work groups during the entire course. In consultation with the coordinator, it is then decided how the missed parts can be made up. If you are absent more often, no final grade will be registered.
| Item and weight | Details |
|
Final grade | |
|
0.7 (70%) Tentamen | |
|
Labwork | |
|
0.3 (30%) Scientific Report |
Practical labwork: Assessment takes place on the basis of the quality of the experimental actions, active attitude during the preparatory assignments and attitude in the lab.
Technical report: The performed wet-lab protocols and the data obtained from them are briefly written down, interpreted and discussed. The assessment takes place on the basis of the quality, correctness and depth of the reported. Associated criteria will be provided during the course.
Test (tentamen): During the literature discussion (journal club) and working groups, assignments are discussed and theoretical backgrounds are discussed. On the last day of the course, a short test is taken in which the knowledge gained here is tested in the form of open questions and/or a few multiple choice questions. This test is "open book" ; you can bring literature, hand-outs and notes taken during the course
Inspection of your grading is possible after the test grade has been announced and will be agreed by e-mail.
Journalclub: For the journalclub you will analyze data from a published primary scientific publication and present and explain one of the figures in a small group. You will not be graded but have to participate.
Labwork: In the lab you will work with dedication on a small project that you will develop yourself and/or in smaller or larger groups. You will formulate your own hypothesis and design, execute and analyze your own Q-RT-PCR experiments. The quality of your data will be graded in the report.
Report: Your hypothesis and data from the experiments will be summarized and placed in the right scientific context in a short report.
The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl
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