Modern DNA Sequencing Methods
http://sandberg.cmb.ki.se/courses/modseq
Aim: After completing the course, the student will understand the technology behind the
major DNA sequencing platforms available today, and their strengths and limitations; and
will know the most important applications, and how they may apply to the student's own
research.
Content: The course will cover the following topics: The history of DNA sequencing.
Introduction to modern DNA sequencing. Practical considerations, cost, dealing with a
deluge of data. Applications - RNA sequencing, ChIP sequencing, metagenomics. Future
technologies and applications.
Format: The course consists of lectures by invited speakers, and a site visit. In addition,
students will be asked to prepare a presentation of how modern DNA sequecning methods
could benefit their own research.
Examination: All lectures are compulsory. In case of absence, lectures can be compensated
by a literature assignment and written report. Oral examination in conjunction with the
presentation of an individual project of research.
Literature: A list of suggested reading for each sub-topic will be published on the course
website (above). The list will be continuously updated. Lecture slides will also be published
on the site.
Location: CMB seminar room, Berzelius väg 35, room A216. See map on last page.
Welcome!
Sten Linnarsson
Assistant Professor, MBB
[email protected]
Rickard Sandberg
Assistant Professor, CMB
[email protected]
Schedule
Monday, March 23
9.00 – 10.30 Introduction
Ass. Prof. Rickard Sandberg & Ass. Prof. Sten Linnarsson
11.00 – 12.30 History of DNA sequencing
Ass. Prof. Sten Linnarsson
13.30 – 15.00 The development of Pyrosequencing and the two different formats: Qiagen
(96- sample format) and Roche (454 technology).
Professor Pål Nyrén, KTH School of Biotechnology
Tuesday, March 24
9.00 – 10.30 Applied Biosystems SOLiD
Inger Jonasson, BA, Lab Manager, Uppsala Genome Center
11.00 – 12.30 The Illumina Genome Analyzer II
Dr. Anna Kiialainen, Department of Medical Sciences, Uppsala University
13.30 – 13.45 General bioinformatics of short reads
Ass. Prof. Rickard Sandberg, CMB
14.00 – 15.00 RNA-Seq
Ass. Prof. Rickard Sandberg, CMB
Wednesday, March 25
9.00 – 10.30 How to read the genetic regulatory code
Prof. MD. Claes Wadelius, Dep. of Genetics and Pathology, Uppsala University
11.00 – 12.30 Metagenomics
Professor Björn Andersson, CMB, KI
13.30 – 17.00 Site visit: 454 core facility, KTH
Hosted by Professor Joakim Lundeberg, KTH
Thursday, March 26
9.00 – 10.30 Sequencing the cancer genome
Assoc. Prof. Tobias Sjöblom, Uppsala University, Dep. Of Genetics and Pathology
11.00 – 12.30 Sequencing of regulatory chromatin regions
Dr. Andreas Lennartsson, Dep. Of Bioscience and Nutrition, KI NOVUM
13.30 – 15.00 High-throughput single-cell RNA-Seq
Ass. Prof. Sten Linnarsson, MBB
Friday, March 27
9.00 – 10.30 Project presentations (20 min per person)
11.00 – 12.30 Project presentations (20 min per person)
13.30 – 14.30 The future of DNA sequencing
Ass. Prof. Sten Linnarsson, MBB
14.30 – 15.00 Wrap-up and course evaluation
Ass. Prof. Rickard Sandberg & Ass. Prof. Sten Linnarsson
Directions to Berzelius väg 35: From Central Station, take bus 47 to its final stop on the
Karolinska campus, then walk 100 m on Berzelius väg to the red circle on the map. From
other places, such as St Eriksplan, take bus 3 and walk 50 m to the red circle.
