The Encyclopedia of DNA Elements (ENCODE)

NCODE 4 seeks to expand the catalog of candidate regulatory elements in the human and mouse genomes through the study of a broader diversity of biological samples including those associated with disease as well as by employing novel assays not used previously in ENCODE. To maximize access to ENCODE data by the research community, all data is shared in databases without controlled access. All newly obtained human biological samples are consented for unrestricted data sharing.  To study the biological function of candidate regulatory elements already compiled by ENCODE, a new component, functional element characterization, has been added in ENCODE 4.

ENCODE 4 includes the following components:

• Functional Element Mapping Centers
  • Conduct high-throughput experiments that map biochemical activities to identify candidate functional elements in the human and mouse genomes.
• Functional Element Characterization Centers
  • Develop and apply generalizable approaches to characterize the role of candidate functional elements in specific biological contexts.
• Computational Analysis Groups
  • Pilot new applications of ENCODE data
• Data Coordination Center (DCC)
  • Processes and shares ENCODE metadata and data, and provide a portal for the community to visualize and download data.
• Data Analysis Center (DAC)
  • Specifies data processing pipelines and quality metrics for major data types, design and perform integrative analysis of ENCODE data to update and refine the Encyclopedia.

For more information, see: ENCODE 4 Participants and Projects.

Read about the ENCODE Pilot Project.

NHGRI has designated the ENCODE Project as a community resource project to accelerate access to and use of the data by the entire scientific community. Accordingly, the data release policy is based on the principle of rapid data release to the scientific community.

External data users may freely download, analyze and publish results based on any ENCODE data without restrictions as soon as they are released. This applies to all datasets, regardless of type or size, and includes no grace period for ENCODE data producers, either as individual members or as part of the Consortium. Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional. The Consortium will continue to publish the results of its own analysis efforts in independent publications. ?We request that researchers who use ENCODE datasets (published or unpublished) in publications and talks cite the ENCODE Consortium in all of the following ways:

1. Cite the Consortium's most recent integrative publication (PMID: 22955616; PMC: PMC3439153);
2. Reference the ENCODE Data Coordination Center (DCC) or GEO accession numbers of the datasets; and
3. Acknowledge the ENCODE Consortium and the ENCODE production laboratory(s) generating the particular dataset(s).

Data Release Policies

• Current ENCODE Consortium Data Release Policy (2014-present)
• ENCODE-modENCODE Consortia Data Release Policy (2008-2014)
• ENCODE Pilot Project Data Release Policy (2003-2007)
• Ft. Lauderdale Agreement on Sharing Data from Large-scale Biological Research Projects: A System of Tripartite Responsibility

The data produced by ENCODE Consortium members are deposited to public databases, including the ENCODE Portal and are available for all to use without restriction. Data users are asked to abide by the ENCODE Data Release Policy when using data produced by ENCODE Consortium members, acknowledging the ENCODE Consortium as specified in the policy.

As the ENCODE Project has increased its study of primary cells and tissues, it has begun working on human biological samples that have been explicitly consented for genomic research and unrestricted sharing of genomic data, in order to maximize the accessibility and utility of ENCODE data. This means that data can be deposited in freely accessible databases, e.g., GEO and the ENCODE Portal and shared without registration or prior approval.

The ENCODE Consortium has developed sample informed consent language that explicitly asks for 1) consent to genomic research and 2) consent to unrestricted sharing of genomic data. Below are links to this sample language as well as two examples of IRB-approved consents allowing for release of genomic data to unrestricted, public databases:

• Sample consent for unrestricted access to genomic data
• IRB-approved consent for unrestricted access to ENCODE data
• IRB-approved consent for unrestricted access to ENCODE data as addendum to consent for pre-existing project

These examples provide the research community with information and examples to assist with the development of informed consent processes and consent forms for genomics-related research projects. They are not provided as guidance or as a template promoted by NHGRI, but as a reference to inform investigators and IRBs considering these issues. It is important to tailor consent documents for each individual study.

For general information from NHGRI about the informed consent process in genomics research, including additional sample consent forms, see: www.genome.gov/informedconsent.

These tutorials were prepared for biologists using human and/or mouse genetic data to study disease, gene regulation, and basic biology. They explain what data are available, what they mean, how they can be displayed and downloaded and how they can be used in genetic research on human disease.

• ENCODE Data Utilization Workshop, October 2018, ASHG
• Navigating the ENCODE Encyclopedia: Exploring Candidate Regulatory Elements, Linked Genes and Genetic Variation with SCREEN, October 2017, ASHG
• ENCODE 2016: Research Applications and Users Meeting
• American Society of Human Genetics 2016: ENCODE DCC Uniform Processing Pipelines
• American Society of Human Genetics 2016: 3D Genome Organization and Chromatin Interaction
• ENCODE: Getting Started
• 2016 Society of Toxicology Annual Meeting Workshop
• ENCODE/Roadmap Epigenomics Tutorial, October 2015, ASHG
• ENCODE 2015: Research Applications and Users Meeting
• ENCODE Workshop, April 2015, Keystone Symposia
• Using the ENCODE Resource for Functional Annotation of Genetic Variants, January - March 2015
• Roadmap Epigenomics Tutorial, March 2015, Keystone Symposia
• Roadmap Epigenomics Tutorial, October 2014, ASHG
• ENCODE Workshop Tutorial, October 2014, ASHG
• ENCODE/Roadmap Epigenomics Tutorial, October 2013, ASHG
• ENCODE Tutorial May 2013, Biology of Genomes, CSHL
• ENCODE/Roadmap Epigenomics Tutorial, November 2012, ASHG
• ENCODE Portal Tutorials

Meetings and Workshops

• ENCODE 2016: Research Applications and Users Meeting
  June 8-10, 2016
• ENCODE 2015: Research Applications and Users Meeting
  June 29 - July 1, 2015
• From Genome Function to Biomedical Insight: ENCODE and Beyond
  March 10-11, 2015
• ENCODE Pilot Project Launch Meeting
  March 7, 2003
• Workshop on the Comprehensive Extraction of Biological Information from Genomic Sequence
  July 23 - 24, 2002

Publications

• Defining functional DNA elements in the Human Genome
  Proceedings of the National Academy of Sciences, April 21, 2014
• Nature ENCODE explorer
  A series of coordinated scientific reports published in the Nature, Sept. 5, 2012 online issue
• A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
  PLoS Biology, April 19, 2011
• Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
  Nature, June 13, 2007
• ENCODE Web Focus
  Related articles on ENCODE from Nature, June 2007
• Special Issue on ENCODE from Genome Research
  June 2007
• The ENCODE (ENCylopedia Of DNA Elements) Project.
  Science, Vol. 306, Issue 5696, 636-640, 22 October 2004.

Features

• Reddit "Ask Me Anything" Recap: The ENCODE Project
  February 17, 2017
• NHGRI to host symposium on model organism Encyclopedia of DNA Elements project
  June 20-21, 2012
• ENCODE RFAs Expand Effort to Understand the Genome
  October 5, 2011
• Funding Now Available for Technology Development to Catalog and Analyze Function of Genomes
  May 25, 2011
• New user's guide and tutorial helps disease researchers interpret human genome
  April 19, 2011

Press Releases

• NIH to expand critical catalog for genomics research
  February 2, 2017
• NIH ENCODE grants advance effort to survey entire human instruction book
  September 24, 2012
• ENCODE data describes function of human genome
  September 5, 2012
• NHGRI to develop revolutionary technologies for exploring genome function
  April 25, 2012
• Researchers Expand Efforts to Explore Functional Landscape of the Human Genome
  October 9, 2007
• New Findings Challenge Established Views on Human Genome
  June 13, 2007
• ENCODE Consortium Publishes Scientific Strategy
  October 21, 2004
• Beyond Genes: Scientists Venture Deeper Into the Human Genome: ENCODE Project Seeks to Identify All Functional Elements in Human DNA
  October 9, 2003
• Launch of Pilot Project to Identify All Functional Elements in Human DNA
  March 4, 2003