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300200 UE DNA sequencing: molecular protocols, Sanger sequencing and NGS (2020W)

a hands-on tutorial

5.00 ECTS (3.00 SWS), SPL 30 - Biologie
Continuous assessment of course work

Registration/Deregistration

Details

max. 12 participants
Language: English

Lecturers

Classes (iCal) - next class is marked with N

Wednesday 07.10. 11:30 - 12:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Monday 19.10. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Tuesday 20.10. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Wednesday 21.10. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Thursday 22.10. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Friday 23.10. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Monday 11.01. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Tuesday 12.01. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Wednesday 13.01. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Thursday 14.01. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Friday 15.01. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Friday 22.01. 09:00 - 13:00 Übungsraum 2 (Fakultätszentrum für Biodiversität) Rennweg 1.OG

Information

Aims, contents and method of the course

Aims: The participants get an overview about the generation of DNA sequences using traditional and advanced methods, and will work with software tools for DNA sequence data analysis.
Content: We will give an overview of the different sequencing techniques and their use in systematic and evolutionary biology with examples from botany. In addition, the advantages, limits and pitfalls over the different technologies in comparison to traditional methods are discussed.
Methods: The students perform practically all main steps from DNA extraction, PCR and sequencing (after Sanger, chain termination method) of provided organismal samples. Other methods of DNA extraction and library preparation methods for Illumina and PacBio sequencing (NGS) are introduced. The generated DNA sequences will be analysed and a phylogenetic framework will be constructed. On the last course day the students will analyse Illumina NGS data which already has been generated beforehand.

Assessment and permitted materials

There is compulsory attendance!
The initial meeting counts as the first teaching unit and therefore compulsory attendance is obligatory! An absence from the initial meeting without prior agreement (email!) causes de-registration from the course by the leader.
Maximum times allowed absent are 1 day (8 hours) per practical week with cogent excuse (e.g. doctor's confirmation letter, mandatory attendance of other courses or exams).

The grading is based on three partial performances (participation, presentation, protocol). Active course participation is to be provided during the practical week, the final presentation on the last course day, and the protocol has to be submitted at a later date.
You must bring a lab coat for the practical laboratory days (not for the initial Meeting and the last course day of presentations)!

Beneficial for a positive graduation are:
(1) Basic lab experience (e.g., handling of piston stroke pipettes).
(2) Basic computational experience.
(3) Knowledge for performing a online literature survey.
(4) Ability for team work (usually in groups of 2).

Due dates for the written protocol:
First dead-line: 12. February 2021 (with a possibility for corrections).
Final dead-line: 26. February 2021 (no possibility for corrections).

Minimum requirements and assessment criteria

The minimum requirements for a positive grading are based on the following partial performances:
(1) Active participation during the course.
(2) Final presentation of the results as a PPT presentation on the last day of the course (ca. 15 min. allotted for speaking + 5 min. discussion).
(3) Preparation of a written protocol in the style of a scientific publication according to the specifications of the course leader with a later submission date.

Assessment of performance:
Each partial performances will be graded individually and will be integrated into the total grading of the course by different percentage points. For a positive total grading a minimum of half of the percentage points for each partial performances have to be reached.
Participation: 12.5% (4 pt.).
Test 1: 12.5% (4 pt.).
Test 1: 12.5% (4 pt.).
Protocol: 62.5% (20 pt).

1 = 29-32 pt.
2 = 25-28 pt.
3 = 21-24 pt.
4 = 17-20 pt.
5 = ≤16 pt.

Examination topics

There will be two intermediate exams.
The protocol has to be prepared with content of the course and additional literature.

Reading list


Association in the course directory

MBO 5, MEC-9, M-WZB

Last modified: Tu 27.10.2020 12:30