Advanced large scale gene expression profiling:
focus on miRNAs, ChIP-on-chip, and whole genome sequencing
Turku, Finland, 19-22 May, 2008
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Organisers
Riitta Lahesmaa, Turku Centre for Biotechnology, Finland
Juhani Soini, Turku Centre for Biotechnology, Finland
Annika Brandt, Turku Centre for Biotechnology, Finland
Introduction
This course continues on from the previous ESF course on large scale expression analysis using DNA microarrays held at the Turku Centre for Biotechnology, Turku Finland, 2004. During this advanced course, we will introduce researchers the most recent development in the methods within the functional genomics field. An important aim for the course is that the participants learn to use novel array based technologies and to exploit these maximally in context of the relevant biological questions. The main goal will be to decrease the threshold for using the available technology by introducing the equipment that are needed to be able to perform the large scale expression experiments, and by practical exercises learn the participants getting started with the subsequent data analysis.The course includes a hands-on training on the most recent large scale expression analysis techniques, two days with basics on miRNA, ChIP-chip method and whole genome sequencing. The third day will be dedicated for data analysis. The course will end with a minisymposium by outstanding speakers in the functional genomics field. The number of course participants is restricted to 24 persons. A limited number of the participants will have an opportunity to analyse their own control and sample RNAs.
The course and the minisymposium is free of charge to all participants.
The National DNA Microarray Centre is the national core facility for the development of microarray technology and production of microarrays in Finland. The Centre collaborates with other biocenters nationally and worldwide. The Centre produces in-house printed glass-based DNA microarray slides and is equipped to provide services on Affymetrix, Agilent, GE Amersham CodeLink and Illumina array platforms. In addition there are available ABIPrism Genetic Analyser sequencing facility and ABIPrism 5700, 7700, 7900HT for Taqman RT-PCR services. The novel Solexa sequencing system by Illumina will be introduced on the course. The Centre organizes, in addition, courses and symposia, and provides DNA microarray services from array production to complete projects.
Monday 19th May
Welcome (Juhani Soini)
View on technology:
-DNA Microarrays (Juhani Soini)
-ChIP-chip method (Lea Sistonen’s Group)
-ChIP-chip case study1 (Malin Åkerfelt)
-ChIP-chip case study2 (Risto Renkonen Group)
-ChIP-chip case study3(Riitta Lahesmaa Group)
-ChIP-chip data analysis (Asta Laiho/Renkonen/Lahesmaa)
Introduction to hands on training day
miRNA isolation (VTT/Olli Kallioniemi’s group)
cDNA synthesis, starting the reactions
Tuesday May 20th
Continuation with the miRNA experiment.
Hands on day, making one slide miRNA microarray experiment /or
performing Taqman miRNA analysis
Whole Genome Sequencing lecture (Petri Auvinen)
Solexa sequencing demonstration (Illumina)
Methods for Phylogenetic classification of organisms (Karp/Sivonen Groups)
Wednesday May 21th
Data extraction Day
Scanning of the slides
Data analysis microarrays (Olli Kallioniemi’s Group)
Data analysis Taqman (Rissanen/Linja)
Data analysis large scale sequencing (Auvinen/Greco)
Thursday May 22nd (Minisymposium)
9:00-11:30 Large scale expression analysis techniques and applications
11:30-12:00 Lunch
12:00-16:00 Bioinformatics and data analysis
16:00 Closing remarks
The course will be held at the Finnish DNA Microarray Centre which is part of the Turku Science Park organization that joins 25 000 students in two universities, university hospital, and polytechnic school with spin-off companies, established business enterprises and production plants in the city of Turku, in which one of the main focus areas is biotechnology – from the education through the research to the production. Turku has a long history as a city with graceful architectural landmarks still standing by the river Aura, The Turku Cathedral (oldest parts date back to Years 900-1200) and the medieval Turku Castle guarding the city in front of one of the largests archipelagos in the world.
Registration
Registration is now closed.
