Practicum Advanced Genomics I
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 of these techniques. In this course, students will perform their own RNA sequencing experiment on P19 cells, that were derived from an intriguing form of cancer termed teratocarcinoma. P19 cells have the capacity to respond to signaling molecules and can differentiate into nearly all cell types of the body. The students will choose, design and execute their own experiment and gain experience with all steps involved in transcriptomics. The basics of the practical work are widely applicable but to facilitate students with different backgrounds three experimental themes can be chosen from: 1) developmental biology, 2) neural differentiation and 3) cancer drug development. 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 the identification of transposable elements in plants to single cell RNA sequencing techniques in mammals. 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.
|
Activiteit |
Uren |
|
Hoorcollege |
2 |
|
Practicum |
68 |
|
Werkgroep |
40 |
|
Zelfstudie |
47 |
|
Toets |
2 |
Programme's requirements concerning attendance (OER-B):
Additional requirements for this course:
Attendance at practicals and working groups is compulsory. Attendance at the introductory lecture 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. As this is not the usual textbook stuff, 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 | |
|
5 (50%) Tentamen | |
|
3 (30%) Technical report | |
|
2 (20%) labwork |
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 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.
Labwerk: In het lab ga je met toewijding, vlot en zelfstandig te werk. Je bereidt het practicum voor en neemt actief deel aan de practicuminstructies en discussies. De kwaliteit van de labresultaten wordt beoordeeld.
Technisch rapport: De uitvoering van de protocollen en de interpretatie/analyse van de data moet op technisch niveau worden gepresenteerd en bediscussieerd. De nadruk ligt hierbij op kwaliteitscontrole en interpretatie van de data en nog niet op de bioinformatica. Zie hiervoor Practicum Advanced Genomics II.
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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The schedule for this course is published on DataNose.