Workshop: Integrating ENCODE Data With Your Research: An Interactive Survey of ENCODE Tools and Resources

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This workshop will introduce participants to three important ENCODE resources: 1) The ENCODE data portal, which hosts raw and processed data from over 15 thousand ENCODE and community experiments, 2) SCREEN, a web-based visualization tool for ENCODE annotations such as the Registry of candidate cis-Regulatory Elements, and 3) Juicebox, an innovative genome browser for visualizing 3D contact data (e.g., Hi-C) at continuous resolutions, in the context of one-dimensional annotations such as genes and regulatory elements.

For more information, visit our Online Program Planner.

Learning Objectives:

  1. Indicate the scope of ENCODE data, annotations, and efforts and state opportunities for integrating this data with personal research
  2. Using the ENCODE data portal, examine how to access raw and processed data from ENCODE experiments.
  3. Using SCREEN, examine collections of regulatory elements and the genes they regulate across hundreds of cell and tissue types.
  4. Using Juicebox, construct how to visualize and investigate 3D genomic interactions in the context of linear genomic, epigenomic, and transcriptomic datasets.

Stephanie Morris, PhD

Program Director

Division of Genome Sciences, NHGRI

Ingrid Youngworth, PhD

ENCODE DCC

Stanford University

Jessica Au

ENCODE DCC

Stanford University

Khine Lin

ENCODE DCC

Stanford University

Meenakshi Kagda, PhD

ENCODE DCC

Stanford University

Jennifer Jou

ENCODE DCC

Stanford University

Bonita Lam, PhD

ENCODE DCC

Stanford University

Forrest Tanaka

ENCODE DCC

Stanford University

Jill Moore, PhD

ENCODE DAC

UMass Medical School

Henry Pratt

ENCODE DAC

UMass Medical School

Neva Durand, PhD

Assistant Professor

Aiden Lab, Baylor College of Medicine

Key:

Complete
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Available
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Section 0: ENCODE introduction
ENCODE: The Encylopedia of DNA Elements
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Section I: The ENCODE Portal
ENCODE Portal Intro
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Portal Navigation, Part 1
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Portal Navigation, Part 2
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Portal Data Collection
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Basic & Advanced Query Building
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Ontologies
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ENCODE Portal Cart Basics Part 1
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ENCODE Portal Cart Basics Part 2
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Section II: Registry of cCREs and SCREEN
Introduction to the Registry of cCREs
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Biological Use Cases of the Registry of cCREs
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SCREEN Walkthrough
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Additional SCREEN details (optional)
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Section III: Juicebox
Introduction
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Loading Maps
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Loading Annotations
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Comparing Maps
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Sharing URLs
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Hosting with Dropbox/Drive/GEO
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Visualizing from the ENCODE Website
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Interactive Figure
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Interactive Figure (Optional)
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Juicebox for Assembly (Optional)
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