About this Class

This 2-day course, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of ChIP-Seq Data Analysis. There will also be a talk on ENCODE and a comprehensive discussion of topics ranging from experimental design to data visualization. This workshop will include presentations on using open source applications (MACS, HOMER, MEME, SICER) as well as commercial software (Genomatix).  To access the NCI Genomatix server, to request for a password through IT helpdesk to genomeanalyzer.nci.nih.gov.

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. This workshop will be remotely telecast to the Library Training Room in Bldg 549 at NCI-Frederick for attendees who select to register at that location. Please register only if you intend to attend the workshop.

Date: May 16-17, 2016 (Monday and Tuesday)

Time: 9:30 am – 12:30 pm and 1:30 – 4:30 pm

Locations:

Live Workshop - NIH Bethesda - Bldg 10, FAES Room 4

Remote Simulcast - NCI-Frederick - Scientific Library Training Room, Bldg 549

Workshop Agenda

Monday, May 16, 2016

Day 1 - Session 1: 9:30 am – 12:30 pm

9:30 am – 11 am

Presenter: Peter Fitzgerald, Ph.D, CCBR, OSTR, NCI

Title:  Introduction to ChIP-Seq

• Introduction
  • Historical Perspective and Technical Variations
  • Experimental methodology
  • Comparison to ChIP-Chip
• Data Analysis
  • Experimental Design
  • Quality Control 
  • Peak Calling (Different methodologies)
  • Major Sources of Error
  • Reasons why Experiments Fail
• Sequence Specific Binding
  • Identification of Motifs
  • Overexpressed sequences
  • Pathways
• Resources
  • Public Repositories
  • Literature References
  • Software listings

11 am – 12:30 pm

Presenter: Bong-Hyun Kim, Ph.D., CCBR, Leidos Biomed

Title: Understanding ENCODE (ENCyclopedia Of DNA Elements)

• ENCODE Guidelines and best practices
• Access policies and data retrieval mechanisms
• Other public databases – Epigenome, Mouse Encode

Day 1 – Session 2

1:30 pm – 4:30 pm

Presenter: Bong-Hyun Kim, Ph.D., CCBR, Leidos Biomed

Title: ChIP-Seq Analysis Workflow

• Data QC metrics, plots and online tools
• Narrow Peak calling algorithms (e.g. MACS)
• Annotation (e.g. HOMER)
• Motif analysis (e.g. MEME)

Tuesday, May 17, 2016

Day 2 – Session 1

9:30 am –12:30 pm

Presenters: Chongzhi Zang, Ph.D., Dana-Farber Cancer Institute

                     Weiqun Peng, Ph.D., George Washington University

Title: Analyzing ChIP-seq data with SICER (Spatial Clustering for Identification of ChIP-Enriched Regions)

• ChIP-seq overview 
• Characteristics of histone mark ChIP-seq data
• SICER algorithm: basic idea and model
• Interactive SICER tutorial (on Galaxy): 
  • Data format and description
  • Run SICER with control
  • Run SICER without control
  • Run SICER for differential peak calling
  • Other useful tools

Day 2 – Session 2

1:30 pm – 4:30 pm

Presenter:  Susan Dombrowski, Ph.D, Genomatix

Title: Peeking into the Biology of your ChIP-Seq Peaks with Genomatix

• Automated ChIP-Seq workflow:
  • Peak Calling: MACS, SICER, NGS Analyzer
Read and Peak Classification
Sequence Extraction
Transcription Factor Binding Site Overrepresentation
Motif Detection: CoreSearch

  • Meta Analysis and Integration of RNA-Seq data with ChIP-Seq peaks
  • Overview of RNA-Seq: Class Demo
  • Positional Correlation of ChIP-Seq peaks with differentially-expressed transcripts
  • Downstream Target Prediction
  • Defining gene regulatory "frameworks" in co-expressed genes

Software requirements for the computer system to run Genomatix:

Files

• Genomatix_ChIPSeq_BTEPWorkshop_May2016.pdf: |
• ChIPseq_SICER_CZ.pdf: |
• BTEP-encode.pptx: |
• Tbx20_ko_vs_wt_-6000_to_11000_extracted_transcripts.xls: |