researchers who are moving beyond the basic information of the reference genome sequence.
ENCODE: Encyclopedia
Researchers are using many cutting-edge technologies to learn as much as possible aboutvariations, genes, non-coding transcripts, regulatory elements, and genome structure and more, inof DNA Elements
UniversityofCalifornia,
Santa
Cruz
GenomeBrowser
extensive
detail acrossthe entire
genome. The UCSC
Genome Bioinformatics Group hosts thewww.encodeproject.org
The ENCODE Project (ENCyclopedia of DNA Elements) is an international consortium ofENCODE DCC, or Data Coordination Center, aspects of the project.

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ENCODE Portal
Human and Mouse (below) data
are available
Experiment Matrix visuallysummarizes types of data
Submitted ENCODE Datasets thatare available to explore

1

Search offers various ways to locate
data of interest

3

ENCODE data is integrated in the
Genome Browser interface
Earliest access to new data via thePreview Browser
See sample visualizations of data
Learn about the resources ENCODE
researchers are using

4

The ENCODE project is funded andcoordinated by the NHGRI. TheUCSC Genome Browser is thedesignated Data Coordination
Center (DCC) for the ENCODE
project and the official ENCODE
data repository.

2All ENCODE data is available todownload and use with other tools orfor other analyses

www.ncbi.
nlm.nih.gov/pubmed/21526222

Mouse cell line and tissue details
Defined and controlled experimental
aspects are described
Target proteins assessed inexperiments are explained
Learn about ENCODE with tutorials,papers, presentations and more

An ENCODE Consortium publication offers great background andways to explore the project data.

5Guidance on experimental strategies
and platform characterizationsDetails of file structures used
Collected information on software
resources associated with ENCODE
data and analysis

321

The ENCODE Experiment Matrix provides an up-to-dateview of the breadth of ENCODE experiments, with aninterface for selecting experiments for viewing in thebrowser or downloading underlying data for analysis

Simple and Advanced search forms to locate
data and tools that meet your specific needs

A downloadable spreadsheet of the data types, celllines, factors, treatments, project teams, accession
numbers, and data restriction dates
45

Examine the responsibilities for using the ENCODE data, andsee how to properly acknowledge and cite it

On the main UCSC Genome Browser, ENCODE data are identified with the NHGRI helix icons.
In the Table Browser the project data sets are all available by name.

Quick Reference Card Copyright © 2012, Version 9-12, OpenHelix, LLC. OpenHelix is a trademark of OpenHelix, LLC. Created through sponsorship by UCSC, with funding from NHGRI.

ENCODE Quick Reference Card
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Data Views
All ENCODE data can bevisualized in the UCSC GenomeBrowser as annotation tracks.

Signals detected in experiments
can be shown in various modes.
Dense mode compresses data into
the most compact display style.
Choosing other visibility types may
provide further details. Full display
offers the most expanded view of
the underlying data, with additionalgraphical details that can provide
signal histogram and designationsof the “peak” locations.

ENCODE data can be visualized andqueried like any other data in theUCSC Genome Browser, across theentire genome. For help with anoverview of the UCSC foundations,see the OpenHelix tutorials thatprovide more background.
This “wiggle” track display shows thesignal level in various cell lines(identified by color) which can beturned on and off (see below)
1

peak

dense

fullsignals

ENCODE tracks can be found inmany track groups. Hyperlinks
provide access to track details,
sometimes as a super-track pagefor a set, or to individual subtracks
for specific technique andexperimental details and filter
options.

Tracks have different
conventions and color codes, butmany will offer both signal
dsiplays of the full results
accross a region, and also showa peak value in that region aswell. Some tracks will offer filters
to set threshold values.

Super-tracks combine related
topic data using different techniques(such as open chromatin state here)that can be evaluated together.

ENCODE data are identified in thebrowser annotation track menu by
the NHGRI helix icon symbol
dense and full and peanutbutter placement text goes
here and there andsometimes nowhere at all.

ENCODE Regulation super-track is an integrated collection ofrelated data types that can help researchers evaluate agenomic region. Transcription levels, histone marks, chromatinstate and transcription factor binding can be quickly displayed.
1

Click on triangle to accessmeta-data for further details
about the experimental scenario
and contributing team.

Users can choose various aspects ofthe experiments to display. Peaks,
signals, individual cell lines, replicates,and various treatment conditions may
be available to select and explore.

For some tracks,
individual cell line
signals will be viewed
as histogram
displays. Users canshow or hide specificcell lines of interestby selecting them.

Super-track and track Description sections will have crucial
meta-data to understand the projects, and will explain the display
conventions, color codes, and more. Citations for data ortechnologies may be provided when available. Credits and contacts
for the project teams willl also be provided.

visit www.openhelix.com/ENCODE2 for
ENCODE tutorials and training materials

www.openhelix.com
or call 1-888-861-5051

The Genomics Knowledge
You Need, When You Need It

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