Education

Transcriptomics & Resequencing
Lectures 1ECT
Lectures & practicals & assignment 3ECT

Date: 25-28 October 2010
Organisers: Department of Biosciences, Institute of Biotechnology, Alan Schulman, Jaakko Kangasjärvi, FGSPB, VGSB
Teachers: Jarko Salojärvi , Jaakko Tanskanen, Lars Paulin & Daniel Nicorici

Lectures: Auditorium 1041 (Biocentre 2) 1015-1215
Monday 25th
Intro lecture on sequencing technologies: Sanger, 454, Illumina, SOLiD (+ Helicos, etc.)
Lars Paulin (Institute of Biotechnology) PDF
Tuesday 26th
Bioinformatics for microarrays: packages, approaches, annotation issues
Jaakko Tanskanen (Institute of Biotechnology) PDF
Wednesday 27th
Expression analysis, RNA-Seq, alternative splicing
Daniel Nicorici (Institute for Molecular Medicine Finland) PDF
Thursday 28th
Next-generation genome sequencing
Jarkko Salojärvi (Department of Biosciences) PDF

Practicals: Viikki Korona Info building teaching labs 138 and 170 14-16
Monday 25th
Tour of DNA sequencing and genomics lab
Petri Auvinen (Institute of Biotechnology) NOTE! Cultivator 2 (Viikinkaari 4)
Tuesday 26th
Annotation demonstrations
Jaakko Tanskanen (Institute of Biotechnology)
Wednesday 27th
Short read alignments from an RNA data set
Daniel Nicorici (Institute for Molecular Medicine Finland)
Thursday 28th
Assembly and SNP discovery from resequencing
Jarkko Salojärvi (Department of Biosciences)

The course project work will be managed through this website:
https://sites.google.com/site/resequencing2010/

The course will cover the following topics:

- planning chips
- different types of replicates
- preparation of RNA for different platforms (chips or sequencing)
- description of methods a) chip hybridisation (Agilent etc.); b) sequencing (454 and solid)
- introduction to the Roche and ABI platforms and their applications
- data analysis
- the difference between data from a sequenced genome and a non-sequenced genome
- EQTL transcript differences
- visit to the core facilities with 454 and solid sequencing equipment