ChIP & RNA-seq practical course 2013
General
The course is for Phd students or postdocs that need to do ChIP-seq and/or RNA-seq for their work. During the course the participants will learn how to do the complete work-flow. The course is split into an experimental part, during which the libraries for sequencing are prepared and submitted for sequencing. Since we want to help for doing "real research" the participants need to bring their own samples. Guidelines for sample preparations will be given at a preparatory meeting. After the libraries have been sequenced the part on data analysis of the results will take place.
- Participants: PhD students and postdocs from the DKFZ or BioQuant
- Location: BioQuant, INF 267
- Wiki with course material detailed information: http://malone.bioquant.uni-heidelberg.de/groups/ngs/
- Organizers: Philipp Mallm & Karsten Rippe
Preparatory meeting (5. 3. 2013, 13:00 - 16:00, seminar room 655, BioQuant 6th floor)
All participants need to provide their own samples for ChIP-seq and RNA-seq analysis. Instructions will be given how to prepare
- cross-linked, fragmented chromatin for ChIP-seq
- DNase-treated total RNA for RNA-seq
- max. 2 ChIP-seq + 2 RNA-seq samples per participant.
Experiments (3 days, 15. 4. - 17. 4. 2013, BioQuant teaching lab)
- strand-specific RNA-seq library
- ChIP of histone modifications
- library preparation with barcode system
- Bioanalyzer and Qbit quality control of libraries
- submission for sequencing.
Data analysis (2 days, 10.6 - 11. 6. 2013, BioQuant seminar room SR044 and computer lab)
- quality control and technical report
- read mapping and visualization
- basic data analysis with open source tools
Teachers
Experiments
- Philipp Mallm: Preparation of samples for ChIP-seq and RNA-seq
- David Ibberson: Preparation of samples for ChIP-seq and RNA-seq, CellNetworks Sequencing Core Facility at BioQuant
- Caroline Marth: Library preparation, ChIP and quality control
- Sabrina Schumacher: Library preparation, ChIP and quality control
- Stephan Wolf: Sequencing at the DKFZ
Data analysis
- Philipp Mallm: Basics of ChIP-seq and RNA-seq analysis
- Benedikt Brors: Peak calling
- Barbara Hutter: Differential gene expression
- N. N. (from DKFZ core facility): Bioinformatical data analysis services at the DKFZ core facility
- Maiwen Caudron-Herger: RNA-seq analysis of small and long non-coding RNAs
- Marc Zapatka: Analysis of deep sequencing data with R and Bioconductor
Application
Due to the logistics for doing the experimental and analysis we can only accept 8-10 participants. Thus, we might have to do a selection from the applications we get. In this case we would give preference to applicants that will "really" need to use these thechniques to move on with their research projects. Thus, we would ask you to provide some information on yourself and why participation at the course would help your research work.
Application to the course:
- Short CV and letter of motivation for attending the course (including which samples you want to analyze)
- e-mail to Philipp Mallm: j.mallm@dkfz.de
- Deadline: 21st February 2013
- Notifications about acceptance will be send by 27th February.
Costs
There is no course fee (thanks to the support from epigentics@dkfz) but participants have to cover the sequencing costs of their samples (~100-200 € per library, depending on sequencing depth) or make individual arrangements for having their libraries sequenced.
Supporters
Doing this course is a lot of work and we would not be able to do it without the support from a lot of people (and we will need some more help as things move on). We are particularly grateful for the help of Angret Jöster and Marc Hemberger with the BioQuant logistics and our supporters from
- epigenetics@dkfz, a cross-topic program at the DKFZ to promote research in epigenetics (to register send an e-mail to epigenetics (at) dkfz.de)
- DKFZ deep-sequencing core facility
- CellNetworks Sequencing Core Facility at BioQuant
- the CancerEpiSys consortium
Useful links
Analysis tools |
Sequencing platforms and kits |
Other links |
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