Sandberg Lab

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

Modern DNA Sequencing Methods

[schedule]

Duration: March 23 - March 27, 2009.

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

Welcome!

Sten Linnarsson                    Rickard Sandberg
Assistant Prof, MBB                Assistant Prof, CMB
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 [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 Tuesday, March 24 9.00 - 10.30 Applied Biosystems SOLiD [pdf] Inger Jonasson, BA, Lab Manager, Uppsala Genome Center
11.00 - 12.30 The Illumina Genome Analyzer II [pdf] Dr. Anna Kiialainen, Department of Medical Sciences, Uppsala University pdfs: Bentley_Nature_08, Mardis_AnnRevGenHumGen_08 13.30 - 13.45 General bioinformatics of short reads [pdf] Ass. Prof. Rickard Sandberg, CMB pdfs: Overview, Eland, MAQ, Bowtie, Novoalign, Tophat, velvet. 14.00 - 15.00 RNA-Sequencing [pdf] Ass. Prof. Rickard Sandberg, CMB pdfs: Wang_NatRevGen_09,Mortazavi_NatMethods_08,Wang_Nature_08 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 pdfs: Johnson_Science_07
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 pdfs: Wood_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 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

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




































 
Locations of visitors to this page