300200 UE DNA sequencing: molecular protocols, Sanger sequencing and NGS (2022W)
a hands-on tutorial
Continuous assessment of course work
Labels
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).
- Registration is open from Th 08.09.2022 14:00 to Th 22.09.2022 18:00
- Deregistration possible until Mo 31.10.2022 18:00
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.
Correction deadline on 17.02.2023
- 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
- Friday 27.01. 09:00 - 18:00 Übungsraum 1 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Information
Aims, contents and method of the course
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.
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.
(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.
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: Fr 27.01.2023 09:50
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.