Sandberg Lab

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

Modern DNA Sequencing Methods


Duration: March 14 - March 18, 2011.
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 14
 9.00 - 9.30   Introduction
               Ass. Prof. Rickard Sandberg & Ass. Prof. Sten Linnarsson
               pdfs: Review

 9.30 - 10.15  History of DNA sequencing [pdf]
               Ass. Prof. Sten Linnarsson
10.30 - 12.00 Applied Biosystems SOLiD [pdf] Inger Jonasson, Lab Manager, and Christian Tellgren-Roth, Bioinformatician, Uppsala Genome Center Platform URL: SOLiD 13.30 - 15.00 Enrichment methods Dr. Olle Ericsson, Dept of Genetics and Pathology, Uppsala University pdfs: Review 15.30 - 17.00 Bioinformatics for next-generation sequencing and introduction to Computer practises. [pdf],[intro-pdf] Ass. Prof. Rickard Sandberg Tuesday, March 15 [in computer labs "Dot" and "Enter"] 9.00 - 12.00 Computer practise 1: ChIP-Seq data analyses pdf 13.00 - 17.00 Computer practise 2: RNA-Seq data analyses pdf Wednesday, March 16 9.30 - 10.30 Studying epigenetics using next generation ChIP and sequencing technologies Assoc. Prof. Ola Hermanson, Neuroscience department, Karolinska Institutet 10.45 - 12.00 Cancer Genomics Prof. Jussi Taipale, KI 13.30 - 15.00 Transcriptome studies using next-generation sequencing [pdf] Ass. Prof. Rickard Sandberg 15.30 - 17.00 High-throughput single-cell RNA-Seq Ass. Prof. Sten Linnarsson, MBB
Thursday, March 17 10.00 - 11.00 Genomics Prof. Joakim Lundeberg, SciLife Lab, KTH/KI/SU 11.30 - 13.00 Site Visit: SciLife lab Science for Life Laboratory KISP (Karolinska Institutet Science Park) Tomtebodav 23A 14.00 - 14.45 Studying genome organization and regulation using next-gen sequencing Dr. Pelin Akan, SciLife lab pdfs: Dekker_2009_science, ChIA-PET Nature,review Friday, March 18 9.00 - 10.30 Project presentations (20 min per person)
11.00 - 12.30 Project presentations (20 min per person)
13.30 - 14.30 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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