Transcriptomics

Uitgebreide vaknaam	Transcriptomics: DNA microarrays and RNAseq
Leerdoelen	At the end of the course, the student is able to: 1. Know how to design a transcriptomics experiment for a biological problem. 2. Apply the proper statistical method for analyzing transcriptome data. 3. Examine the results by coupling the data to biological knowledge using literature data. 4. Show plans for downstream research. 5. Work accurately on RNA isolation, cDNA synthesis and library preparation for NGS 6. Interpret and analyze RNA-seq data 7. Use statistics in Excel and R and perform shell scripting on a High Performance Computing (Peregrine) system 8. Evaluate problems, progress and results with the other course students, PhD students and teachers. 9. Summarize results and research strategy in a PowerPoint presentation and a report.
Omschrijving	In this course, theory and practical’s are combined to give an in-depth view in the of transcriptomics research on prokaryotes in answering questions in modern molecular genetics and -biology research. The projects selected for this course are based on research questions of PhD students and post-doctoral fellows of the department of Molecular Genetics. In principle the experiment have not been done before, which means that the generated data is novel. This master course is divided into three parts. The first part focuses on the experimental design of a biological experiment, the theoretical background of Next Generation Sequencing (DNA-Seq and RNA-Seq) and on how transcriptomics data is used in research. Students will grow bacteria according to the experimental design and isolate RNA from the various samples. The second part consists of quality control of the RNA and the library preparation for all samples to will be loaded on a Next Generation Sequencing machine to generate the transcriptome data. On the basis of lectures on specific software, statistics and High Performance Computing, required for transcriptome analyses, the students will analyze their own datasets. During the third part of the course, the analyzed data will be coupled to biological knowledge by using additional statistical methods and students will draw conclusions from their analyses. Also, based on their findings, the students will be encouraged to propose ideas for further experiments.
Uren per week
Onderwijsvorm	Hoorcollege (LC), Practisch werk (PRC), Werkcollege (T) (All parts of this course are mandatory. During the lectures the necessary information for preforming the statistics and practicals will be explained. Missing a part without consulting the coordinator will result in not succeeding the course.)
Toetsvorm	Practisch werk (PR), Presentatie (P), Verslag (R) (Final grade is points/10 ; Assignment 1, short talk (15) + Assignment 2, Shell Scripting (5) + Logbook (15) + Report (50) + Oral presentation (15))
Vaksoort	master
Coördinator	dr. A. de Jong
Docent(en)	D. Incarnato, PhD. ,prof. dr. J. Kok
Verplichte literatuur	Titel Auteur ISBN Prijs A syllabus will be used during the course
Entreevoorwaarden	The course assumes prior knowledge acquired from Microbiology & Genetics research or equivalent.
Opmerkingen	Students from the degree programme Biomolecular Sciences have priority, to register please send an email to: academicadvisor.mscbio@rug.nl Course coordinator: dr Anne de Jong, anne.de.jong@rug.nl, 050 363 2047 Location: Research group Molecular Genetics (GBB), Centre for Life Sciences. Students in Biomolecular Sciences have priority for this course. capacity: 24 students Dit vak had vorig jaar vakcode MLBB017A
Opgenomen in	Opleiding Jaar Periode Type MSc Biology: Research  (Compulsory master courses) - semester II a keuze MSc Biology: Science, Business and Policy  (Compulsory master courses) - semester II a keuze MSc Biomolecular Sciences  ( Compulsory courses general programme (3 out of 8)) - semester II a keuzegroep MSc Biomolecular Sciences  (Electives/Optional modules) - semester II a keuze MSc Ecology and Evolution: Ecology and Conservation  (Electives/optional modules) - semester II a keuze MSc Ecology and Evolution: Evolutionary Biology  (Electives/optional modules) - semester II a keuze