Course Details

  • Date: April 17th, 2017 - April 18th, 2017
  • Time: 9:30 am - 4:00 pm
  • Location: Bldg 10 FAES room 4 (B1C205)
  • Presenter(s): Alexei Lobanov (CCBR), Peter FitzGerald (GAU), Thomas Werner (Genomatix)

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. 
Date: April 17-18, 2017 (Monday and Tuesday)
Time: 9:30 am to 4:00 pm
Location: NIH Bldg 10 FAES Classroom 4 (B1C205)
Registration required. Please click on ‘Register Here’ link at the bottom of this webpage.


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
    • Pathways
  • Resources
    • Public Repositories
    • Literature References
    • Software listings
11:30 am – 12:30 pm               An Overview on Experimental Subtypes and Variations of ChIP-Seq
                                                 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.
Some of the specific subtypes that will be presented include:
  • DNase-seq
  • 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
12:30 – 1:00 pm                       LUNCH BREAK   


Day 1 Afternoon

1:00 – 4: 00 pm              Analysis of ChIP-Seq data: Raw Data to Results
                                       Presenter: Bong-Hyun Kim, PhD, CCBR
This session will cover, in comprehensive detail, the analytical pipeline that is implemented by CCBR. After reinforcing critical aspects and best practices to conduct an effective ChIP-Seq experiment, attendees will have the opportunity to follow a demo of the CCBR ChIP-Seq workflow using an example dataset. There will be detailed review of data QA/QC, visualization of results and the types of outputs from the pipeline.

Day 2 Morning

9:30 am -12:30 pm     Hands-on Tutorial for Analysis of ChIP-Seq data with the Genomatix Genome Analyzer (GGA)
                                    Presenter: Thomas Werner, PhD

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.

At the end of the workshop, participants will be able to:
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
3. Do further downstream analysis by selecting peaks (bed files), converting them to sequence files, and use FrameWorker to find putative MORE (Multiple Organized Regulatory Elements) cassettes.
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

1:30 – 3: 30 pm          Mining ChIP-Seq data from Public Databases
                                   Presenter: Bong-Hyun Kim, PhD, CCBR
In this session, attendees will be able to learn how to explore information from publicly available ChIP-seq databases, and extract meaningful data that could be used for your research. Some of the databases to be discussed are:
  • RegulomeDB
  • ENCODE (ENCyclopedia Of DNA Elements)
  • Epigenome Roadmap
  • Mouse Encode & modENCODE
  • Cistrome
  • JASPAR database