Probing DNA-Protein Interactions
This 2-day workshop, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of ChIP-Seq data analysis. Topics to be covered include: experimental design; read alignment; peak calling; and biological interpretation. A hands-on component will include tutorials on Genomatix, and a demo of the CCBR ChIP-Seq pipeline (featuring MACS and SICER). There will also be a session on mining public data from ENCODE and other databases.
NOTE: This is a BYOC (Bring your own laptop Computer) class. Government issued or personal computers are permitted. We will be able to supply a very limited set of computers, so if you want to take the class but cannot bring your own computer please indicate such in the Comment section on the registration form.
Day 1 Morning
9:30 – 11:30 am Introductory Lecture
Presenter: Peter FitzGerald, PhD – CCR, NCI
The opening talk on ChIP-Seq will introduce the fundamentals and best practices for the technology, and provide the foundation for:
- Understanding the methodolgy
- Comparisons to related techniques
- Data Analysis
- Experimental Design
- Quality Control
- Peak Calling (Different methodologies)
- Major Sources of Error
- Causes of Fail Experiments
- Validation Methods
- Sequence Specific Binding
- Identification of Motifs
- Overexpressed sequences
- Public Repositories
- Literature References
- Software listings
Presenter: Alexei Lobanov, PhD, CCBR
This talk will highlight innovative variations of the classical ChIP-Seq technique that provide different insights and information to analyze the epigenome. There will be discussion on the experimental differences, considerations to choose a subtype based on the research question, and considerations to analyze the data generated from these techniques.
- Assay for Transposase-Accessible Chromatin-seq (ATAC-seq)
- Formaldehyde-assisted Isolation of Regulatory Elelments–seq (FAIRE-seq) reveal regions of open chromatin, not associated with any protein
- MNase-seq identifies specifically positioned nucleosomes
Day 1 Afternoon
Day 2 Morning
The presenter will guide participants through hands-on-training with a ChIP-Seq experiment on the GGA software tool. The training will cover aspects from analysis of BAM files through annotation & statistics, use visualization tools from the Genomatix GePS pathway system and Genome Browser, and finish with a higher level downstream promoter analysis.
1. Set up and generate a graphical overview of a ChIP-seq workflow that will include loading a sample data set into the workflow, discussion of parameters, executing the analysis, and examining the results.
2. Analyze results using:
Annotation & Statistics application to gain a deeper understanding of their content
Correlation of ChIP-Seq peaks with actual transcriptional changes to define real Transcription Factor (TF)-targets
Analysis of these target genes using GePS (Genomatix pathway system)
Data visualization in feature-rich Genome Browser
4. Use ModelInspector to determine whether a MORE-cassette is relevant for the biology in question.
12:30 – 1:30 pm LUNCH BREAK
Day 2 Afternoon
ENCODE (ENCyclopedia Of DNA Elements)
Mouse Encode & modENCODE