ENCODE Genome-Wide Data on
the UCSC Genome Browser	

Melissa Cline	

ENCODE Data Coordination Center (DCC)	

UC Santa Cruz	

http://encodeproject.org	

Slides at http://genome-preview.ucsc.edu/	What is ENCODE?	

• International consortium project with the goal of
cataloguing the functional regions of the humangenome	

GTTTGCCATCTTTTG!
CTGCTCTAGGGAATCCAGCAGCTGTCACCATGTAAACAAGCCCAG
GCTAGACCAGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCC
ACCACAGGCATGAGT• A gold mine of experimental data for
independent researchers with available disk space	ENCODE covers diverse regulatoryprocesses	

ENCODE experiments areplanned for integrative analysis	Example of ENCODE data	Genes	

Dnase HS	

Chromatin Marks	

Chromatin State	Transcription	

Factor Binding	Transcription	

RNA Binding	Translation	

ENCODE tracks on the UCSC
Genome Browser	

ENCODE tracks
marked with the
NHGRI helix	There are currently 2061 ENCODE experiments at the ENCODE DCC 	How to find the data you want	Finding ENCODE tracks the hard way	

A better way to find ENCODE tracks	Finding ENCODE metadata descriptions	Visualizing: Genome Browser tricks thatevery ENCODE user should know	Turning ENCODE subtracks andviews on and off	

Peaks	Signal	View on/off 	

Subtrack	

on/off	Right-click to the subtrack display menu	Subtrack Drag and Drop	Sessions: the easy way to save andshare your work	Downloading data with less pain	1. Via the Downloads button on
the track details page	2. Via the File Selection tool	Publishing: the ENCODE data
release policy	Every ENCODE subtrack has a“Restricted Until” date	Key points of the ENCODE data
release policy	

• Anyone is free to download and analyze data.	

• One cannot submit publications involvingENCODE data unless 	– the data has been at the ENCODE DCC for at least ninemonths, or	– the data producers have published on the data, or	– the data producers have granted permission to publish.	

• Please acknowledge the ENCODE project and thedata producers in all publications.	

Additional Resources	• The OpenHelix ENCODE tutorial at
http://www.openhelix.com/ENCODE/ 	

• A User's Guide to the Encyclopedia of DNA
Elements (ENCODE) in PLoS Biology	

• The ENCODE Project page at
http://www.genome.gov/10005107	

• The UCSC Genome Browser User’s Guideat http://genome.ucsc.edu/goldenPath/help/	Acknowledgements	

• Cat Herding: Kate Rosenbloom and Jim Kent	

• Cats: Galt Barber, Tim Dreszer, Katrina Learned,Venkat Malladi, Brian Raney, Cricket Sloan,Vanessa Swing, and Matt Wong 	

• Systems: Jorge Garcia, Victoria Lin, and ErichWeiler	

• The UCSC Genome Browser staff	

• The ENCODE consortium	

• Funding: NHGRI	The End	

Bonus Slides	

ENCODE and related projects	

ENCODE Pilot Project:	

hg16, hg17, hg18	

(1% of the human genome)	

ENCODE Project: hg18, hg19	

(full human genome)	

ENCODE ARRA
Grants: hg19	

Mouse ENCODE	ARRA Grants:mm9	modENCODE Project 	(fly and worm genomes)	

2003	

2004	

2005	

2006	

2007	

2008	 2009	

2010	

2011	

2012	

ENCODE Data Lifecycle	

Data Coordination Center(DCC)	

Genome Preview Browser	

Data	Production	

Labs	

http://genome-preview.ucsc.edu	

Data Wrangling	

DataAnalysis
Center	

Quality Assurance	

Genome Browser	

http://genome.ucsc.edu	

NCBI
GEO	

ENCODE Track Organization	

Supertracks 	

Tracks 	

Subtracks	

8 in hg19	

45 in hg19	

1584 in hg19	

ENC RNA-Seq	

Caltech RNA-seq	 GM12878 - strand-specific, GM12878 paired, H1hESC - strand-specific, …	

CSHL Long RNA-seq	 GM12878-Nucleus, K562-Nucleoplasm,
HepG2-Cytosol, HSMM-WholeCell, …	Riken CAGE-Loc	 GM12878-Nucleus, K562-Polysome,
NHEK-Cytosol, BJ-WholeCell, …	

ENC Histone	

Broad Histone	 GM12878-CTCF, K562-H3K4me1,
HepG2-H3K9ac, HSMM-H2A.Z, …	

UW Histone	 GM12878-H3K4me3, K562-H3K27me3, 	

HUVEC-H3K36me3, BJ-H3K4me3, …	

…	…	 ….	

Rectangular region-select	Display settings explained	

Dense	

Squish	

Pack	

Full	

Dense	

Squish	Pack	Full	3. Via NCBI GEO