Sandberg Lab

Ludwig Institute for Cancer Research & Department of Cell and Molecular Biology, Karolinska Institutet

Modern DNA Sequencing Methods


Duration: March 8 - March 12, 2010.
Location: CMB seminar room, Berzelius väg 35, room A216. See map below.

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 is in conjunction with the presentation of an individual project of research.


Sten Linnarsson                    Rickard Sandberg
Assistant Prof, MBB                Assistant Prof, CMB


Monday, March 8
9.00 - 10.30   Introduction
               Ass. Prof. Rickard Sandberg & Ass. Prof. Sten Linnarsson
               pdfs: Review

11.00 - 12.30  History of DNA sequencing [pdf]
               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). [pdf] Professor Pål Nyrén, KTH School of Biotechnology pdfs: Nyren_MMB_07, Margulies_Nature_05, Ronaghi_Science_1998
15.30 - 17.00 Applied Biosystems SOLiD [pdf] Inger Jonasson, Lab Manager, and Christian Tellgren-Roth, Bioinformatician, Uppsala Genome Center Platform URL: SOLiD
Tuesday, March 9 11.00 - 12.30 Enrichment methods Dr. Olle Ericsson, Dept of Genetics and Pathology, Uppsala University pdfs: Review 13.30 - 14.15 Bioinformatics in next generation sequencing projects [pdf] Ass. Prof. Rickard Sandberg, CMB links: Overview, MAQ, Bowtie, Novoalign, Tophat, velvet. 14.30 - 15.15 RNA-Sequencing [pdf] Ass. Prof. Rickard Sandberg, CMB pdfs: Wang_NatRevGen_09,Mortazavi_NatMethods_08,Wang_Nature_08
Wednesday, March 10 9.00 - 10.30 Sequencing the cancer genome Assoc. Prof. Tobias Sjoblom, Dep. of Genetics and Pathology, Uppsala Univ. pdfs: Wood_Science_07
11.00 - 12.00 Metagenomics Professor Björn Andersson, CMB, KI
13.00 - 14.30 High-throughput Biology Prof. Jussi Taipale, Dep. of Biosciences and Nutrition, KI NOVUM
15.00 - 17.00 Site visit: Illumina Sequencing Machine Hosted by Sten and Rickard, MBB
Thursday, March 11 9.00 - 10.30 How to read the genetic regulatory code Prof. MD. Claes Wadelius, Dep. of Genetics and Pathology, Uppsala University pdfs: Johnson_Science_07
11.00 - 12.30 Sequencing of regulatory chromatin regions Dr. Andreas Lennartsson, Dep. Of Bioscience and Nutrition, KI NOVUM pdfs: Jiang_NatRevGen_09
13.30 - 15.00 High-throughput single-cell RNA-Seq [pdf] Ass. Prof. Sten Linnarsson, MBB
Friday, March 12 9.00 - 10.30 Project presentations (20 min per person)
11.00 - 12.30 Project presentations (20 min per person)
13.30 - 14.30 Science for Life Laboratory (Next-gen sequencing core facility) Prof. Joakim Lundeberg, KTH
14.30 - 15.00 Wrap-up and course evaluation Ass. Prof. Rickard Sandberg & Ass. Prof. Sten Linnarsson

Additional Course Links:
Sequencing Platforms Links: Illumina/Solexa, SOLiD, 454
Forum: SEQanswers

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