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300200 UE DNA sequencing: molecular protocols, Sanger sequencing and NGS (2022W)

a hands-on tutorial

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

Registration/Deregistration

Note: The time of your registration within the registration period has no effect on the allocation of places (no first come, first served).

Details

max. 12 participants
Language: English

Lecturers

Classes (iCal) - next class is marked with N

The practicalis held as an on-site course in two parts (weeks).
Please note the COVID regulations of the University of Vienna valid at the time. Only come to the dates in good health!
Preliminary meeting: 05.10.2022 (First course unit!).
1 week: Data collection in the laboratory: 17.10.2022-21.10.2022.
2 week: Data analysis on the computer: 23.01.2023-27.01.2023.
Protocol submission deadline on 24.02.2023.

Wednesday 05.10. 11:30 - 12:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Monday 17.10. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Tuesday 18.10. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Wednesday 19.10. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Thursday 20.10. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Friday 21.10. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Monday 23.01. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Tuesday 24.01. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Wednesday 25.01. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Thursday 26.01. 09:00 - 18:00 Übungsraum 1 (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 (QIAGEN), libray preparation (Illumina or NEB) and sequencing (Illumina) of provided organismal samples. Other methods of DNA extraction (CTAB), sequencing (after Sanger, chain termination method) and library preparation methods for Illumina, Nanopore (e.g. MinION) and PacBio sequencing (HTS/NGS) are introduced. The generated NovaSeq Illumina-DNA sequences will be analysed in the second partical week (pastid or chromosome assembly) and a phylogenomic framework will be constructed.

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 time allowed absent is 1 day per practical week (2 days in total for the whole course) 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, mini tests, protocol). Active course participation is to be provided during the practical week, each of the two mini tests on the last course day of each week, and the protocol has to be submitted at a later date.
You must bring a lab coat for the practical laboratory days of the first week (not for the initial meeting and the second practical week).

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: 24. Frebruary 2023.

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) Two mini tests at the end of each practical week.
(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 04.10.2022 21:09