15 Nov 2010 - New ENCODE Tutorial at OpenHelix
OpenHelix, together with the UCSC Genome Bioinformatics group, anounce a new online
tutorial suite to teach users how to access the ENCODE data in the UCSC Genome
Browser. This tutorial introduces the types of data available under ENCODE, and
presents methods to access the data via the Genome Browser, Table Browser, and
downloads. This tutorial suite is freely available at
16 September 2010 - First Production ENCODE Data on hg19 has been Released
We are pleased to announce the release of the first sets of production ENCODE data
GIS DNA PET: This track shows the starts and ends of DNA fragments from
different cell lines determined by paired-end ditag (PET) sequencing using different
DNA fragment sizes for analysis of genome structural variation. The data in this
track uses the new BAM data format. For more information about SAM/BAM, click
here. All of the subtracks
that comprise this track were originally released on hg18 and have been remapped to
This track (version 4, May 2010) shows high-quality manual annotations merged with
evidence-based automated annotations across the entire human genome generated by the
GENCODE project. Previous versions of this data were released on hg18, but this
newest version is available solely on hg19.
20 August 2010 - New ENCODE Integrated Regulation Super-track Released
We are pleased to announce the release of the ENCODE Integrated
Regulation super-track, a collection of regulatory tracks containing
state-of-the-art information about the mechanisms that turn genes on and
off at the transcription level. Individual tracks within the set show
enrichment of histone modifications suggestive of enhancer and promoter
activity, DNAse clusters indicating open chromatin, regions of
transcription factor binding, and transcription levels. When viewed in
combination, the complementary nature of the data within these tracks
has the potential to greatly facilitate our understanding of regulatory
The data comprising these tracks were generated from hundreds of
experiments on multiple cell lines conducted by labs participating in
the ENCODE project, and were submitted to
the UCSC ENCODE Data Coordination Center for display on the Genome
Faced with the problem of how to display such a large amount of data
in a manner facilitating analysis, UCSC has developed new visualization
methods that cluster and overlay the data, and then display the
resulting tracks on a single screen. Each of the cell lines in a track
is associated with a particular color. Light, saturated colors are used
to produce the best transparent overlay.
Currently, the ENCODE Regulation data are available only on the
March 2006 (NCBI Build 36, UCSC version hg18) assembly of the human
For a detailed description of the datasets contained in this super-track
and a discussion of how the tracks can be used synergistically to
examine regions of regulatory functionality within the genome, see the
track description page.
6 August 2010 - June and July ENCODE news
Initial Release of the
track: This track shows short
tag sequencing of cDNA obtained from biological replicate samples
(different culture plates) of the ENCODE cell lines. The sequences
were aligned to the human genome (hg18) and UCSC known-gene splice
Release 2 of the
track: This track shows alignments, signal density, and
splice sites based on 75 bp paired reads and 32 bp strand-specific
single reads of polyA+ RNA aligned to the human genome (hg18) and
UCSC known-gene splice junctions. Also included with the track as
downloadable files are RPKM expression level measurements at the
gene-level and exon-level, and candidate novel exons. Release 2
of this track adds five new cell types: H1-hESC, HeLa-S3, HepG2,
HUVEC, and NHEK.
Initial Release of the
GIS PET Loc
track: This track shows starts and ends of full length
mRNA transcripts determined by PET sequencing of polyA+ and total
RNA from 6 subcellular compartments and whole cell, in 8 cell lines.
Release 2 of the HAIB TFBS
track: This track shows signal density and binding sites
of selected transcription factors in a variety of cell types.
Release 2 of this track adds 73 new experiments covering 13 new cell
lines and 27 antibodies. Additionally, DEX and EtOH treatments have
been included in the A549 cell line.
Initial Release of the BU ORChID
track: This track displays the predicted hydroxyl
radical cleavage intensity on naked DNA for each nucleotide in the
Update of the Mapability
track: This track displays the level of sequence
uniqueness of the reference hg18 genome. The update adds CRG
Alignability data, which displays how uniquely k-mer sequences align
to a region of the genome.
19 July 2010 - April and May ENCODE news
Initial Release of the GIS RNA-seq
track: This track shows RNA-seq of high-quality PolyA+
RNA in ENCODE Tier1 cell lines and H1 ESC sequenced on the ABI Solid
Release 3 of the Yale TFBS
track: This track shows probable binding sites of the
specified transcription factors (TFs) in the given cell types as
determined by chromatin immunoprecipitation followed by high
throughput sequencing (ChIP-Seq). Release 3 adds 64 experiments
and 26 input/control datasets for a total of 54 factors in 21 cell lines.
Release 2 of the RIKEN CAGE Loc
track: This track shows 5' cap analysis gene expression
(CAGE) tags and clusters in RNA extracts from different sub-cellular
localizations. Release 2 of this track adds data for eight new
cell-type/compartment combinations (GM12878 Nucleus, H1-hESC whole
cell, HepG2 cytosol/nucleus/nucleolus, HUVEC cytosol, and NHEK
Initial Release of the Duke Affy Exon
track: This track shows gene expression by microarray of
RNA extracted from 28 cell lines that were also analyzed by DNaseI
hypersensitivity, FAIRE, and ChIP assays (Open Chromatin track).
Initial Release of the UW DNase DGF
track: This track shows high-resolution DNase
annotations from samples sequenced to depths of 300-fold or greater,
in 5 cell lines.
Initial Release of the GIS DNA PET
track: This track shows the starts and ends of DNA
fragments from different cell lines determined by paired-end ditag
(PET) sequencing using different DNA fragment sizes for analysis of
genome structural variation.
18 March 2010 - February and March 2010 ENCODE news
Release 3 of the Open Chromatin
track: This track displays evidence of open chromatin in
multiple cell types from the Duke/UNC/UT-Austin/EBI ENCODE group.
Release 3 of this track includes 18 new cell line or cell/treatment
experiments. In addition, a number of new experiments were added to
existing cell lines. Almost all Peaks have been called anew using
improved cut-offs and p-Values. Finally, a second type of peak
called using a ZINBA algorithm has been provided for several of the
Release 3 of the Broad Histone
track: This track shows maps of chromatin state
generated using CHIP-seq. Release 3 of this track adds the HSMM cell
line and includes new experiments for H1-hESC and NHLF.
of the UW Affy Exon track:
This track displays
human tissue microarray data using the
Affymetrix Human Exon 1.0 GeneChip. This release includes 28 new cell types, and replaces the data for four existing tables (replicate 1 for K562, NB4, and SKMC; replicate 2 for HeLa-S3).
of the UW Histone track:
This track displays
maps of histone modifications genome-wide in different cell lines, using ChIP-seq high-throughput sequencing.
Release 2 of the HudsonAlpha
Release 2 adds data for five new cell
Release 3 of the Gencode
Genes track: shows high-quality
manual annotations in the ENCODE regions generated by the
Version 3 of the
Gencode gene set presents a full merge between HAVANA and ENSEMBL,
giving priority to the manually curated Havana objects and using
ENSEMBL objects where they are different or fall into un-annotated
Initial release of the CSHL
RNA-seq track: This track depicts
NextGen sequencing information for RNAs between the sizes of 20-200 nt
isolated from RNA samples from tissues of sub cellular compartments
from ENCODE cell lines.
Release 3 of the UW
DNaseI HS track:
This track shows
DNaseI sensitivity measured genome-wide in different using the Digital DNaseI
methodology, and DNaseI hypersensitive sites. This
release includes 19 new cell lines as
well as new version of NB4 replicate 1.
6 January 2010 - December 2009 ENCODE news
"ENCODE whole-genome data in the UCSC Genome Browser":
This paper addresses the history of the ENCODE project, summarizes the datasets
available as of September 2009, and outlines methods to access the data. See
Nucleic Acids Res. 2010 Jan;38(Database issue):D620-5.
Initial release of the
track: This track contains sequence reads and RPKM transcript abundance
measures for sequences that map to either the genome or to known RNA splice sites.
The results of four different mapping algorithms are provided, enabling
comparison between different mapping algorithms. Results are available for
polyA+ and total RNA for the two ENCODE Tier 1 cell lines.
Release 2 of the
track: This track displays maps of chromatin state generated using CHIP-seq.
Release 2 adds data for the ENCODE Tier 2 cell lines H1-hESC and HepG2, plus
NHLF (normal human lung fibroblasts) and HMEC (human mammary epithelial) cells. This
expands the track data to 9 cell lines, and 11 antibodies plus an input control.
Release 2 of the
CSHL Long RNA-seq
track: This track depicts sequencing of long RNAs of more than 200
nucleotides in length. Release 2 adds data from strand-specific assays of
total RNA for the two ENCODE Tier 1 cell lines.
Release 2 of the
ENCODE Open Chromatin
track: This track displays evidence of open chromatin as identified by two
complementary methods, DNaseI hypersensitivity and FAIRE, combined with ChIP
identification methods. Release 2 adds data from eight additional cell types,
expanding the track to 41 experiments in 13 cell lines.
7 November 2009 - October ENCODE News
Sep 2009 data freeze complete: The ENCODE Consortium has just
completed data submissions for the fourth production data freeze (Sep 09). The first
set of data from this freeze to complete quality review is now available on the UCSC
public server, in Release 2 of the
ENCODE Transcription Factor Binding Sites from Yale/UC-Davis/Harvard
track. Release 2 adds 59 ChIP-seq experiments to this track.
Other October track releases: The
Affymetrix/CSHL Subcellular RNA Localization by Tiling Array
track was expanded to include 4 additional experiments.
encodeproject.org: By request of the ENCODE Consortium, the domain
encodeproject.org has been registered by the ENCODE Data Coordination Center,
and is redirected to the ENCODE portal at UCSC.
New grants funded: NHGRI has funded 5 new ENCODE grants, as part
of the American Investment and Recovery Act. The new grants include expansion of
ENCODE to the mouse genome and proteogenomics.
Job openings at UCSC: The UCSC Genome Browser and ENCODE projects
are currently accepting applications for
Software Developer and
Biological Database Testing/User Support Technician
positions. We are looking for talented individuals who would like to use their
skills in computer science, biology, and bioinformatics on fast-paced projects
featuring the work of top genomics scientists worldwide.
24 September 2009 - ENCODE data releases since July 1
During this period a total of 10 new ENCODE tracks were released to the UCSC public
server. Functional elements and region characterization in these tracks include:
For track names and file access, see the Release Log and Downloads
links listed in the left menu bar.
We would like to thank the contributing ENCODE labs and the the DCC team at UCSC for their efforts
completing these tracks.
1 July 2009 - ENCODE data releases for the period April - June 2009
The following ENCODE tracks were released to the ENCODE DCC/UCSC public server during this period:
The Release Log listed in the left menu bar shows all released ENCODE tracks.
We would like to thank the HudsonAlpha, Transcriptome, Open Chromatin, Broad, and SUNY ENCODE
groups and the DCC team at UCSC for their efforts completing these tracks.
13 March 2009 - ENCODE Data Release: Transcription Factor Binding Sites from Yale/UC-Davis/Harvard
We are pleased to announce the release to the ENCODE DCC/UCSC public server
ENCODE Transcription Factor Binding Sites by ChIP-seq from Yale/UC-Davis/Harvard
(Yale TFBS, in the Regulation group).
This track shows probable binding sites of 12 transcription factors
and RNA polymerase II in 7 cell types, as determined by chromatin
immunoprecipitation followed by high-throughput sequencing.
The Genome Browser displays discrete Peaks
of enrichment and Signal graphs of enrichment density for these
The sequence reads, quality scores, and sequence alignment coordinates from
these experiments are available for
We would like to acknowledge the efforts of the Yale/UC-Davis/Harvard
ENCODE group and the work of the UCSC data wrangler for this group,
Tim Dreszer, for completing this track. We also thank
the entire UCSC ENCODE team and the UCSC Quality Assurance
group for contributing to this first ENCODE track release.
27 Feb 2009 - ENCODE February 2009 data freeze
The February 2009 ENCODE data freeze supplements the data contributed for the
November 2008 freeze, and will be used together with the earlier freeze
for the initial analysis effort of the ENCODE Consortium. Data from
this freeze is being incorporated into tracks created from the first
data freeze, and is being reviewed by the UCSC Quality Assurance team.
9 Dec. 2008 - First ENCODE whole-genome data freeze completed
The ENCODE Consortium has just completed the first freeze
(November 2008) of whole-genome experimental data
produced for the ENCODE production phase. Data submitted
to the DCC for this freeze include:
- transcription factor binding sites
- histone modifications
- DNaseI hypersensitive sites
- DNA methylation
- transcription maps and tags, localized to subcellular
- GENCODE gene annotations
Experiments during this freeze focused on the ENCODE
Tier1 cell lines -- K562 leukemia, and GM12878 lymphoblastoid
(which is also a
1000 Genomes project
sample designated for in-depth analysis of genetic variation).
The freeze also includes data
from some ENCODE Tier2 and Tier3 cell lines (see
Cell Types). The majority
of these experiments were assayed by high-throughput
sequencing (ChIP-seq, DNase-seq, and RNA-seq).
The UCSC quality team is currently reviewing these data.
When the review is complete, the browser tracks and
associated downloads will be released to the UCSC public
Thanks to the many labs who contributed data for the
initial phase of this project. We'd also like to acknowledge
the UCSC ENCODE team for data wrangling during the freeze,
and for the development and maintenance of
the ENCODE automated data submission pipeline and
associated tools: Kate Rosenbloom, Tim Dreszer, Larry Meyer,
Michael Pheasant, Ting Wang, Galt Barber, and Andy Pohl.
4 Oct. 2007 - ENCODE Genome Browser Released for hg18 Assembly
The ENCODE browser for UCSC human genome assembly hg18
(NCBI Build 36) is now available. You can access the browser
or by clicking the ENCODE link on the Genome Browser
home page, then
selecting the Regions (hg18) item in the sidebar menu on
the ENCODE portal page.
The hg18 ENCODE browser includes 540 data tables in 59
browser tracks that were migrated from the hg17 browser.
The hg17 data coordinates were converted to hg18 coordinates
using the UCSC liftOver process.
To improve the accessibility of the data, related ENCODE
tracks have been gathered into new configuration groupings
("super-tracks") that can be displayed or hidden
using a single visiblity control. We have also reduced the
number of track groups and have modified some of the group
names for clarity.
The following table
summarizes the data currently present in the hg18 ENCODE
|Regions and Genes||2||12||73|
Note that the Variation and Comparative Genomics data were
not lifted during this migration; instead, they will be
replaced by new data. The first ENCODE MSA alignment for
hg18 (TBA) is currently in progress on the UCSC
During the migration, ENCODE tracks with whole-genome
data were moved into the standard browser track
groups. These include the GIS PET and UCSD/LI
TAF1 tracks. Future submissions of whole-genome ENCODE data
will be loaded directly into the standard track groups.
We have expanded the ENCODE downloads site to include
original data for all "wiggle" datasets. These
data files now have filename extensions indicating the
wiggle input format (fixed step, variable step, or
You can find a description of the migration project and
full details of the tables, tracks, and super-tracks
available at the UCSC ENCODE portal on the UCSC
The UCSC team members who contributed to this effort were:
Andy Pohl (data conversion and database loading), Ting Wang
and Donna Karolchik (super-track documentation), Bob Kuhn
(portal updates), Brooke Rhead, Kayla Smith, and Ann Zweig (quality
assurance), and Kate Rosenbloom (super-track development,
13 Jun. 2007 - ENCODE Findings Published in Nature and Genome Research
The findings of the ENCODE project have been
released to the public today, the culmination of a
four-year effort to catalog the biologically functional
elements in 1 percent of the human genome. The publications,
which include a group paper in the 14 June 2007 issue of
Nature and 28 companion papers
in the June 2007 issue of
Genome Research, were authored by
researchers from academic, governmental, and industry
organizations located in 11 countries. The Nature
issue includes a pull-out poster featuring a screenshot of
the UCSC Genome Browser displaying a broad range of the
In the press release accompanying the publication
NHGRI Director Francis S. Collins is quoted as saying
"This impressive effort has uncovered many exciting
surprises and blazed the way for future efforts to explore
the functional landscape of the entire human genome. Because
of the hard work and keen insights of the ENCODE consortium,
the scientific community will need to rethink some long-held
views about what genes are and what they do, as well as how
the genome's functional elements have evolved. This could
have significant implications for efforts to identify the
DNA sequences involved in many human diseases."
For more information on the ENCODE project,
including the consortium's data release and accessibility
policies and a list of NHGRI-funded participants, see the
NHGRI ENCODE website.
12 Jun. 2007 - Spring 2007 ENCODE News
Between January and May of 2007, several new or upgraded
data tracks were released by UCSC:
- Gencode March 2007 Genes and Gencode
Reannotation of 69 loci consisting of 132 transcripts
based on RACE, array, and sequencing analyses. New features
include the addition of PolyA features, polymorphic
gene type, and integration of experimental intron
- Yale ChIP-chip RFBR --
Analysis of ChIP-chip data to identify regulatory factor
binding regions, resulting from over 105 experiments
representing 29 transcription factors in 9 cells lines,
performed in 7 labs using 3 microarray platforms. Data
provided by the ENCODE Transcriptional Regulation analysis
- University of Virginia DNA Replication Origins --
Three new datasets representing two new experimental
methods for origin mapping (bubble trapping and nascent
strand) in HeLa and GM06990 cells.
- University of Vienna RNAz --
RNA secondary structure prediction as predicted by RNAz,
based on evolutionary conservation and thermodynamic
- Duke DNaseI Hypersensitivity --
DNase-chip results in IMR90 (fibroblast), K562 (leukemia)
and H9 (stem) cells.
- UCSC EvoFold -- Replaces TBA23 EvoFold.
- UC Davis ChIP Hits -- Updated cMyc and E2F1.
Thanks to the UCSC staff who worked on these tracks:
Rachel Harte and Kate Rosenbloom (development), and Ann
Zweig, Archana Thakkapallayil, and Kayla Smith (quality
9 Jan. 2007 - Winter 2006 ENCODE News
To improve communication, we have posted instructions for
our ENCODE ftp site on the ENCODE Wiki and have set up an
email alias for notifying UCSC about your ENCODE data
The current UCSC recipients are Kate Rosenbloom, Daryl
Thomas, Ting Wang, and Rachel Harte.
During November and December, four new/improved data tracks
Chip-PET from the Genome Institute of Singapore -
Genome-wide data for c-Myc in P493 B cells was added as a
new subtrack (cMyc P493, encodeGisChipPetMycP493) to the
existing GIS ChIP-PET track.
DNaseI Hs from Duke University -
Existing NHGRI data and new data from the Crawford lab at
Duke University (raw and p-value data for the HepG2 cell
line) were merged into the Duke/NHGRI DNase track. The
newer data is based on DNase-chip technology.
STAGE tags from University of Texas -
Raw tags data for STAT1 in HeLa cells were added
as a new subtrack (UT STAT1 HeLa Tags,
to the existing UT-Austin Stage track.
DNaseI Hs from University of Washington -
The existing three UW/Regulome DNaseI Sens tracks were
replaced with a single new track (UW/Reg QCP DNaseI Sens)
based on quantitative chromatin profiling (QCP) methods in
16 cell types.
Thanks to the UCSC staff who worked on these tracks:
Rachel Harte, Kate Rosenbloom, and Hiram Clawson
(development), Ann Zweig, Brooke Rhead, and Kayla Smith
7 Oct. 2006 - Comparative Genomics Data Release
Twelve tracks of data produced by the ENCODE Multi-Species
Sequence Analysis group have been released to the UCSC
public server. These tracks contain multiple sequence
alignments, conservation, and conserved (constrained)
elements produced by four conservation methods
(phastCons, binCons, GERP, SCONE) applied to three sequence
alignments (TBA, MLAGAN, MAVID), and also an assessment of
the agreement among the alignment methods. The alignments
were based on genomic sequence in the ENCODE regions of 28
vertebrate species, as defined in the
MSA September 2005 sequence freeze.
The following tracks can now be found in the ENCODE
Comparative Genomics track group on the public ENCODE
- MSA Consensus Constrained Elements
- TBA Alignments, TBA Conservation, TBA Conserved Elements
- MLAGAN Alignments, MLAGAN Conservation, MLAGAN Conserved
- MAVID Alignments, Conservation, Conserved Elements
- MSA Alignment Agreement, MSA Alignment Gaps
Thanks to the following providers of this data:
- Elliott Margulies (NHGRI) - TBA alignments, binCons and
phastCons conservation, Consensus elements, sequence freeze
- Daryl Thomas (Haussler lab, UCSC) - sequence freeze
- George Asimenos (Batzoglou lab, Stanford University) -
- Colin Dewey (while at the Pachter lab, UC Berkeley) -
- Greg Cooper (while at the Sidow lab, Stanford
University) - GERP conservation
- Saurabh Asthana (Sunyaev lab, Harvard Genetics) -
- Ariel Schwartz (Pachter lab, UC Berkeley) - Alignment
Also, thanks to the UCSC team that produced these tracks in
the browser: Kate Rosenbloom (track development), Ann Zweig,
Kayla Smith, and Archana Thakkapallayil (quality review).
31 Aug. 2006 - Summer ENCODE data activity
Since mid-June, UCSC has released new ENCODE data from three
labs (Sanger Institute, Uppsala University, and University
of North Carolina) and has a track in
progress for newly submitted data from a fourth lab
Sanger ChIP-chip (MOLT4 and PTR8 cells) - Eight new
datasets were added to the Sanger Chip/chip track.
The new data show sites of H3 histone methylation and
acetylation in MOLT4 (lymphoblastic leukemia) and also
in the chimpanzee PTR8 cell line, used for comparative
analysis. Thanks to Rob Andrews at the Ian Dunham lab
for providing these data.
Uppsala University Chip/chip Butyrate - This
track shows the effects of Na-butyrate treatment of
HepG2 (liver carcinoma) cells on histone H3 and H4
acetylation, assayed on Sanger microarrays. Thanks to Adam
Ameur at the Claes Wadelius lab for providing these data.
University of North Carolina FAIRE (Peaks data
This track was updated to include a subtrack of peaks
generated by an alternate peak-finding algorithm,
ChIPOTle. The FAIRE data were generated from 2091
fibroblast cells hybridized to NimbleGen ENCODE arrays.
Thanks to Paul Giresi at the Jason Leib lab for providing
NHGRI DNaseI-HS Raw (in progress) - DNase-chip raw
and p-value data in GM06990, CD4+, and Hela S3 cells.
Thanks to our UCSC staff who worked on these tracks:
Rachel Harte and Hiram Clawson (development), Ann Zweig
and Archana Thakkapallayil (quality review), and Donna
The ENCODE data status page has been updated to reflect the
14 June 2006 - New ENCODE data at UCSC
During the build-up to the analysis paper submissions,
UCSC received a flurry of ENCODE data submissions
(6 during the month of May). We have recently
released three data sets to our public server;
the remaining tracks are in progress, as indicated below.
Sanger ChIP-chip (HFL-1 cells) -
New data added to the Sanger ChIP track show the
location of modified histones in HFL-1 (embryonic lung
fibroblast) cells. Thanks to Rob Andrews and
Christopher Koch for providing this data.
DLESS (Detection of LinEage Specific Selection) -
This track shows elements predicted by the DLESS program
to be under lineage-specific selection, based on
alignments of 17 mammalian species from NHGRI/PSU
TBA ENCODE alignments. DLESS is based on a phylo-HMM
with states for neutrally evolving and conserved regions,
and for gains and losses on each branch of the tree.
Thanks to Adam Siepel of Cornell University, who
developed the DLESS program, generated the data, and
loaded the annotation track.
UW/Regulome Dnase/Array -
This track displays DNaseI sensitivity in GM06990 cells,
using the DNase/Array methodology. Dnase/Array is a novel
method for isolating DNA segments corresponding to
specific DNaseI cleavage events on individual nuclear
chromatin templates. Thanks to Scott Kuehn at the
University of Washington for providing these data.
Thanks to our UCSC staff who worked on these tracks:
Rachel Harte (development), Ann Zweig, Kayla Smith,
and Archana Thakkapallayil (quality review).
In quality review:
- UNC FAIRE Peaks (Update, 2091 fibroblasts)
- University of Uppsala Chip/Chip (butyrate treatment in HepG2)
- UW/Regulome QCP Dnase HS (update and new cell lines -- 16 tissues)
- PECAN Alignments from EBI
The ENCODE data status page has been updated to reflect the
13 January 2006 - Release of October freeze data complete
All datasets submitted for the October 2005 ENCODE freeze
have now been released. The tracks with their release
- 13 Jan. - Yale ChIP-chip (5 new transcription factors)
- 3 Jan. - University of Uppsala Chip/chip (data correction)
- 2 Jan. - Yale RNA (update)
- 29 Dec. - U Virginia DNA Replication Timing and Predicted Origins
- 28 Dec. - UT Austin STAGE
- 21 Dec. - Affy RNA and Transfrags (HeLa update)
- 22 Nov. - Sanger ChIP-chip (5 histone modifications)
- 19 Nov. - UC Davis ChIP-chip (Pol2, Myc) in HeLa
- 18 Nov. - U North Carolina FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)
- 1 Nov. - Affy RNA and Transfrags (update)
- 1 Nov. - UT-Austin Ng ChIP-chip (E2F4, c-Myc factors)
- 1 Nov. - GIS PET RNA (update)
- 1 Nov. - Gencode Genes and Introns (update)
- 1 Nov. - NHGRI DNaseI HS (update and new GM06990)
- 27 Oct. - UCSD/LI Ng ChIP-chip (update and new TFs)
- 14 Oct. - GIS ChIP/PET (STAT1)
- 21 Sep. - Boston University ORChID (update)
Posted on 17 Oct. 2005 - ENCODE hg17 Genome Browser Released
The ENCODE browser for UCSC human genome assembly hg17
(NCBI Build 35) is now available at
and from the
item in the left (blue bar) menu of the ENCODE portal.
All datasets originally submitted in hg17 coordinates for
the June data freeze were directly loaded; the remaining
data were coordinate-converted using the UCSC liftOver
process. A total of 351 data tables were loaded into our
NOTE: Many of these tracks will be updated with new
data from the October ENCODE data freeze.
Many thanks to all the ENCODE consortium members who
contributed data for this release. We'd also like to
thank UCSC team members Kate Rosenbloom for portal and
track development and Jennifer Jackson, Kayla Smith, Ann
Zweig, and Bob Kuhn for quality assurance.
Posted on 15 July 2005 - Regulome DnaseI HS, Oxford Recombination, and MSA Data Released
The remaining datasets submitted for the June 2005 ENCODE
data freeze have now been released as annotation tracks in
the hg16 browser. These tracks and their release dates are:
- 15 Jul. - TBA23 EvoFold RNA Structure Predictions
- 14 Jul. - Regulome DNaseI HS and Sens
- 14 Jul. - Regulome Plate Q/A and Amplicons
- 14 Jul. - MSA Consensus Elements
- 14 Jul. - TBA alignments with Conservation
- 14 Jul. - Stanford MLAGAN Alignments and Conservation
- 13 Jul. - Oxford Recombination
Posted on 12 July 2005 - EGASP genes, RIKEN CAGE tags, and Stanford RTPCR, ChIP-chip and DNA Methylation data released
Several new ENCODE data sets have been released in the UCSC
EGASP Full, Partial, and Update: These three
gene prediction tracks are from the ENCODE Gene Annotation
Assessment Project (EGASP) Prediction Workshop 2005.
The EGASP Full track shows 20 sets of gene predictions
originally submitted for the workshop, covering all 44
ENCODE regions. THE EGASP Partial track shows eight sets of
gene precdictions that were submitted for the workshop, but do not cover all ENCODE regions. The EGASP Update track
shows updated versions of some of the submitted predictions.
Thanks to Julien Lagarde at IMIM for providing the EGASP
Full and EGASP Partial data sets. Thanks to Tyler Alioto of
IMIM (GeneID-U12 and SGP2-U12), Deyou Zheng of Yale (Yale
Pseudogenes), Sarah Djebali of Ecole Normale Supérieure
(Exogean), Jonathan Allen of TIGR/Univ. Maryland (Jigsaw)
and Mario Stanke of the University of Gottingen (Augustus)
for providing their EGASP Update gene sets.
RIKEN CAGE Predicted Gene Start Sites: This track
shows the numbers of 5' cap analysis gene expression (CAGE)
tags that map to the genome at specific locations. Areas in
which many tags map to the same region may indicate a
significant transcription start site. Thanks to Albin
Sandelin at RIKEN and the FANTOM (Functional Annotation
of Mouse) Consortium for providing these data.
Stanford RTPCR: This track displays absolute
transcript copy numbers for 136 genes and 12 negative
control intergenic regions, determined by real-time PCR in
Stanford ChIP-chip, Stanford ChIP-chip Smoothed
Score: These tracks display raw scores and
sliding-window mean scores for regions bound by the Sp1
and Sp3 transcription factors in three cell lines (HCT116,
Jurkat, K562), assayed by chromatin immunoprecipitation and
hybridization to Nimblegen oligo tiling arrays. The
Smoothed Score track is provided solely for visualization
purposes -- the raw scores should be used for data analysis.
Stanford Methylation Digest: This track displays
experimentally determined regions of unmethylated
CpGs in eight cell lines (BE2C, CRL1690, HCT116, HT1080,
HepG2, JEG3, SNU182, and U87MG). Genomic DNA was digested
with a cocktail of six methyl-sensitive restriction enzymes,
size-selected, amplified, labeled, and hybridized to
Nimblegen oligo tiling arrays.
Thanks to Nathan Trinklein for providing the Stanford
We'd like to acknowledge the work of the UCSC Genome
Bioinformatics team members who produced these tracks:
Kate Rosenbloom, Angie Hinrichs, and Hiram Clawson
(development), Ann Zweig, Bob Kuhn, Galt Barber, Rachel
Hart, and Ali Sultan-Quarrie (quality review), and Donna
Posted on 6 July 2005 - NHGRI DIPs, HapMap SNPs, Sanger Assoc annotation tracks released
The first datasets in the ENCODE Variation group are now
available in the UCSC browser.
NHGRI Deletion/Insertion Polymorphisms: All human
trace data from NCBI's trace archive were aligned to the
genome and processed using the programs ssahaSNP and
ssahaDIP to detect deletion and insertion polymorphisms.
Thanks to Jim Mullikin at NHGRI for performing the analyses
and providing these data.
HapMap Allele Frequencies: This track shows allele
frequencies for the four HapMap populations in the ten
ENCODE regions that have been resequenced for variation
(manually selected regions m010, m013, and m014 and
randomly selected regions r112, r113, r123, r131, r213,
r232, and r321). These data were obtained from HapMap
public release #16c.1. Thanks to the International HapMap
Project for making this information available.
Sanger Genotype-Expression Association: This track
displays associations among gene expression data from the
60 unrelated Centre d'Etude du Polymorphisme Humain (CEPH)
individuals of the International HapMap Project with SNPs
genotyped by HapMap,
in eight ENCODE regions (m010, m013, m014 and r123, r131,
r213, r232, and r321). The CEPH population is composed
of Utah residents with ancestry from northern and western
Europe. The expression data were generated with the
Illumina platform at the Wellcome Trust Sanger Institute.
Thanks to Manolis Dermitzakis at the Sanger Institute for
providing these data.
We'd also like to acknowledge the UCSC ENCODE team members
who worked on these tracks: Heather Trumbower, Daryl Thomas,
and Angie Hinrichs (development), Galt Barber and Ali
Sultan-Qurraie (quality assurance), and Donna Karolchik
Posted on 23 June 2005 - Yale and Affymetrix ChIP-chip and transcription data release; New ENCODE track groupings
To aid ENCODE analysis and reduce visual clutter, we have
split the Genome Browser ENCODE track group into six new
All of these track groups are visible on the UCSC test
browser. The last two groups, Variation and Comparative
Genomics, do not yet have published tracks on the public
server and therefore are not visible on that server.
- ENCODE Regions and Genes
- ENCODE Transcript Levels
- ENCODE Chromatin Immunoprecipitation
- ENCODE Chromosome, Chromatin and DNA Structure
- ENCODE Variation
- ENCODE Comparative Genomics
We have also released a set of new Yale
data and an extensive update of Affymetrix data. The track
controls for these datasets can be found in the
track groups ENCODE Transcript Levels and ENCODE Chromatin
Yale ChIP-chip and RNA: Three tracks of ChIP-chip
data from Yale, evaluating microarray platforms, have been
released: Yale ChIP pVal, Yale ChIP Sig, and Yale ChIP
Sites. These tracks show results of ChIP experiments using
STAT1 antibody in HeLa cells on four different microarrays
-- three custom maskless photolithographic oligo arrays,
designed at different resolutions, and the PCR amplicon
array developed by the Ren lab at the Ludwig Institute/UCSD.
Two tracks of RNA transcript data from Yale have been
released: Yale RNA and Yale TAR. These tracks show
transcriptionally active regions and transcribed
fragments for three cell types (neutrophil, placenta, and
NB4 variously treated for differentiation).
Thanks to Joel Rozowsky at Yale for providing this data.
Additional Yale ChIP-chip data is currently under review by
our quality assurance group.
Affymetrix ChIP-chip and RNA:
The Affymetrix ChIP-chip dataset now contains experimental
results for ten factors (Brg1, CEBPe, CTCF, H3K27me3,
H4Kac4, P300, PU1, Pol2, RARA, and SIRT1) in HeLa cells at
four timepoints after retinoic acid treatment, plus TFIIB
for the final timepoint only. The data is displayed in
eight tracks: Affy PVal 0h, 2h, 8h, 32h and Affy Sites 0h,
2h, 8h, 32h. We acknowledge that this track grouping
is a bit awkward and are working composite track
enhancements to provide more flexibility.
The Affy RNA tracks show RNA abundance and transfrags in
retinoic acid-stimulated HL-60 cells at four timepoints,
and in GM06990 and HeLa cells: Affy RNA Signal and Affy
Thanks to Stefan Bekiranov and Srinka Ghosh at Affymetrix
for providing these data.
Thanks also to the UCSC ENCODE
team members who developed and reviewed these tracks and
to Rachel Harte in the UCSC browser group
for her assistance with track review.
Posted on 15 June 2005 - Six data sets released in Genome Browser
Six more ENCODE annotation tracks have been added to the
Genome Browser this week:
NHGRI DNaseI-Hypersensitive Sites (update): The
NHGRI DNaseI-HS track has been updated with new data. The
track now includes DNaseI-hypersensitive sites in CD4+
T-cells before and after activation by anti-CD3 and
anti-CD28 antibodies. Thanks to Greg Crawford at the
Collins lab (NHGRI) for providing these data.
Genome Institute of Singapore PET of PolyA+ RNA:
The GIS PET RNA track displays starts and ends of mRNA
transcripts determined by paired-end ditag sequencing in
two cell lines, MCF7 and HCT116 treated with 5
fluoro-uracil. A total of 584,624 PETs were generated for
MCF7 and 280,340 were generated for HCT116. More than
80% of the PETs in each group were mapped to the genome.
Thanks to Atif Shahab, Yijun Ruan, the GIS, and the
Bioinformatics Institute of Singapore for providing these
Gencode Gene Annotations and Intron Validation:
The Gencode Genes track displays high-quality manual
annotations in the ENCODE regions generated by the
GENCODE project. A companion track, Gencode Introns,
shows experimental gene structure validations for these
annotations. Thanks to the HAVANA team at the Wellcome
Trust Sanger Institute; France Denoeud, Julien Lagarde,
and Roderic Guigo at the IMIM; and Alexandre Reymond
at the University of Geneva for providing the
annotations and experimental confirmation, as well as
working with UCSC to develop the track display.
Boston University Hydroxyl Radical Cleavage:
The BU ORChID track displays predicted hydroxyl radical
cleavage intensity on naked DNA for each nucleotide in
the ENCODE regions. The prediction algorithm draws data
from a database of 150 experimentally-determined cleavage
patterns. Thanks to Jay Greenbaum at the Tullius lab for
providing these data.
UC Davis ChIP-chip: The UCD Ng E2F1 track shows
ChIP analysis of HeLa cells using E2F1 antibody as
assayed on Nimblegen arrays. The E2F1 factor is associated
with cell cycle control, transcriptional regulation, and
apoptosis. Thanks to the Farnham lab and Kyle Munn, Todd
Richmond and Roland Green of Nimblegen for providing
Ludwig Institute/UCSD ChIP-chip:
Three tracks of ChIP-chip data using Nimblegen arrays
have been released: LI Ng TAF1 IMR90, LI Ng Validation,
and LI Ng gIF ChIP. The TAF1 track shows genome-wide
TAF1 binding sites as determined by ChIP in IMR90
(fibroblast) cells assayed on Nimblegen high-density
oligo arrays. The peaks from the genome scan experiments
were verified using four antibodies associated with
transcription start (Pol2, H3ac, H3K4me2, and TAF1) on
condensed arrays covering the putative TAF1 binding sites.
The gIF track shows the results of ChIP-chip experiments
using gamma interferon-treated HeLa cells, with Pol2 and
Two additional tracks, LI ChIP Various and LI gIF ChIP,
display ChIP-chip data assayed on Ren lab ENCODE PCR
tiling arrays for five antibodies (Pol2, TAF1, H3K4me2,
SUZ12, H3K27me3) and four cell lines (HeLa, THP1, IMR90,
HCT116), as well as gamma interferon experiments using
seven antibodies (Pol2, TAF1, H3K4me2, H3K4me3, H3ac,
H4ac, and STAT1) in HeLa cells.
Thanks to Chunxu Qu and Bing Ren, at the Ren lab for
providing these data and assisting with track display
We'd also like to acknowledge the UCSC team members who
developed these tracks: Kate Rosenbloom, Hiram Clawson,
and Angie Hinrichs for track development; Bob Kuhn, Ali
Sultan-Qurraie and Galt Barber for quality assurance;
and Donna Karolchik and Jim Kent for documentation.
Posted on 9 June 2005 - Sanger Histone Modification ChIP-chip track updated
The Sanger Institute has submitted ChIP-chip data for
additional antibodies and cell lines, which we have
incorporated into the existing Sanger ChIP browser track.
The expanded track now contains data for five antibodies
(H3K4me1, H3K4me2, H3K4me3, H3ac, H4ac) and two cell
lines (GM06990, K562 (leukemia)).
Thanks to Rob Andrews and Chris Koch at the Dunham lab
for providing these data. UCSC team members who developed
this track include Hiram Clawson (track development), Ali
Sultan-Qurraie (quality assurance), and Donna Karolchik
and Jim Kent (documentation).
Posted on 6 June 2005 - Changes to ENCODE track labels in Genome Browser
We have modified the Genome Browser labels for the
existing ENCODE data tracks to trim overly-long labels
that were truncated in the display and to facilitate
cross-track analysis. The new label format shows the
submitter and the experiment, followed by the cell line
(in tracks where the data includes only one cell line).
Posted on 6 June 2005 - Stanford Promoters and UVa DNA Replication tracks released
We are pleased to announce the first UCSC Genome Browser
tracks released for the June 2005 ENCODE data freeze:
Stanford Promoters and UVa DNA Replication Temporal
Stanford has provided an update of their promoter activity
data based on transient transfection luciferase reporter
assays of 643 putative promoter fragments in the ENCODE
regions. The update includes two additional cell lines
and activity averaged across all cell lines. The data
tables now contain additional experimental detail to
facilitate analysis. This track, containing 17 subtracks
(16 cell lines and the average), is labeled "Stanf. Promoter". Thanks to Sara Hartman at
the Myers lab for providing these data.
The Dutta lab at Univerity of Virginia (UVa) has completed
the second biological replicate of their temporal
profiling of HeLa cell replication products and has
provided a dataset containing merged data from the two
replicates. The track, containing five subtracks
representing two-hour intervals, is labeled
"UVa DNA Rep". Thanks to Christopher Taylor at
the Dutta lab for providing these data.
We'd also like to acknowledge the UCSC team members who
worked on these annotation tracks: Angie Hinrichs (track
development), Galt Barber and Ali Sultan-Qurraie (QA), and
Jim Kent and Donna Karolchik (track documentation).
Posted on 24 May 2005 - New MSA sequence data freeze available
A new ENCODE MSA sequence data freeze is available on the
UCSC downloads server. The latest freeze contains
sequences from 23 vertebrates provided by NISC, Baylor,
the Broad Institute (2X) and the whole genome shotgun
(WGS) assemblies. The data may be downloaded as
individual data files or a
Aligners are encouraged to upload alignments and related
data (such as conservation scores and elements) to the
UCSC ENCODE ftp site as soon as possible and then notify
Other data, (conservation, trees, etc.)
will be generated based on this dataset.
The following is a summary of data updates from the
The human assembly version remains at hg16 (Jul. 2003).
The mouse assembly has been updated from mm5 (May 2004) to
mm6 (Mar. 2005).
The multiple rat sequences have been replaced by a single
sequence: rn3 (Jun. 2003).
The cow sequences have been updated using an assembly of
BAC-based sequences provided by Baylor College of
Fugu (fr1), macaque (rheMac1), opossum (monDom1),
Tetraodon (tetNig1), Xenopus (xenTro1), and zebrafish
(danRer2) have been added. The macaque sequence was
obtained from a Baylor
College of Medicine assembly that has not yet been
A new NISC species, rfbat
(Rhinolophus ferrumequinum), is now available.
Platypus data from regions
where NISC has not yet generated data were provided by
Jim Mullikin from a preliminary assembly of Washington
University WGS reads.
This freeze includes low-redundancy sequence data from
tenrec, elephant, armadillo, and rabbit. Only one set of
sequences are provided per species/target combination;
where available, NISC data is provided instead of
the 2X assemblies. These data are not yet accessioned at
NCBI, but were made available by the Broad Institute
(rabbit, elephant, armadillo) and Jim Mullikin (tenrec).
Orthology predictions for Fugu were made only by
MAVID/Mercator; predictions for all other assemblies
supported by the UCSC Genome Browser represent a union
with UCSC predictions as well. Because no additional
post-processing was done on the Fugu predictions, they
contain a few very small contigs.
Thanks to the many people, particularly Elliott Margulies
and Daryl Thomas, who made this release possible.
Posted on 24 May 2005 - ChIP-PET/GIS annotation track (Genome Institute of Singapore) released
The ENCODE Genome Browser now features the ChIP-PET/GIS
annotation track, which shows paired-end
ditag (PET) sequences derived from 65,572 individual p53
ChIP fragments of 5-fluorouracil (5FU) stimulated HCT116
(colon) cells. Only PETs with a single specific mapping
to the genome are included in this track.
Thanks to Atif Shahab, Chia-Lin Wei, and Yijun Ruan at the
Genome Institute of Singapore for
providing the p53 ChIP-PET library and sequence data. The
data were mapped and analyzed by scientists from the
Genome Institute of Singapore, the Bioinformatics
Institute, Singapore, and Boston University. For more
information about this annotation, see the ChIP-PET/GIS
track description page.
Posted on 23 May 2005 - Boston University First Exon annotation track released
The First Exon/BU annotation track, contributed by the
ZLAB at Boston University, is now
available in the UCSC Genome Browser. This track displays
expression levels of computationally identified first
exons and a constitutive exon of 20 genes in the ENCODE
For each gene, all alternative first exons were identified
based on manual selection of predictions from the
program. The expression levels of exons were then
quantified using rcPCR in ten normal human tissues.
Thanks to Ulas Karaoz and the Zhiping Weng lab at
Boston University for providing these data. For more
information about this annotation, as well as a complete
list of the individuals who contributed to this track,
see the First Exon/BU track description page.
Posted on 7 May 2005 - ENCODE status page now available
A simple summary page has been added to the UCSC ENCODE
portal to show the status of datasets submitted to UCSC by
ENCODE contributors. The page may be found at
http://genome.ucsc.edu/ENCODE/trackStatus.html and can be accessed via
links on the ENCODE home page and the ENCODE data
submission page. The status page will be updated
approximately once a week.
To review the latest ENCODE data releases, see the
Posted on 6 May 2005 - UCSD/Ludwig Institute histone modification ChIp/Chip data released
Two additional sets of ChIp/Chip data from UCSD/Ludwig
Institute are now available:
These tracks display locations of acetylated H3 and
dimethylated K4H3 binding in IMR90 (lung fibroblast)
To consolidate viewing in the browser, the previously
released eight datasets from UCSD/LI have been reformatted
as two composite tracks (one track per antibody) with
each track containing four subtracks (one per cell line).
These tracks are:
To facilitate data analysis, the data were also reloaded
in a format that allows extraction of the original data
values via the UCSC table browser.
Thanks to Chunxu Qu and the
lab for providing these data.
Posted on 17 Feb. 2005 - ENCODE downloads released
The ENCODE download area has been reorganized and updated
on our public download server. The downloads access page
and the annotations are now located in the
assembly-specific download directory, currently:
Any web pages referencing the previous UCSC ENCODE
downloads will need to be updated. Please contact us if
you have any difficulties.
Posted on 2 Feb. 2005 - Affymetrix ChIp/Chip and PolyA RNA data released
A second set of ENCODE ChIp/Chip data is now available on
the July 2003 human genome assembly:
ChIp/Affy Pol2 Pval
ChIp/Affy Pol2 Sites
These tracks show RNA Polymerase II precipitation and
RNA abundance in retinoic acid-stimulated HL-60 cells at
0, 2, 8, and 32 hours, as measured by Affymetrix tiling
arrays in the non-repetitive ENCODE regions. The
Pval and Signal tracks show values
for each tiled probe; the Sites tracks show
contiguous regions of enrichment.
A new composite track display was developed to
concisely display multiple data sets of similar types, a
common feature of ENCODE data. Each of these new tracks
contains 4 subtracks, one for each time interval. The
subtracks share a single description page and set of
visibility controls. Checkboxes on the track
configuration page allow selected subtracks to be hidden
in the display.
These data were generated and analyzed by Tom Gingeras'
Kevin Struhl's group at Harvard Medical
School. We would like to thank Stefan Bekiranov at
Affymetrix for submitting the data and working closely
with us to clarify the experimental methods and
Posted on 5 Nov. 2004 - First ENCODE data tracks in the UCSC Browser
The first datasets submitted for the ENCODE project are
now publicly available:
These tracks are visible in the ENCODE track group of the
July 2003 (hg16) human genome assembly. We would like to
thank the labs of Bing Ren (LI/UCSD), Anindya Dutta (UVA),
Rick Myers (Stanford), and Francis Collins (NHGRI) for
contributing the initial ENCODE data sets.
ChIP-chip and transcription (Ludwig Institute/UCSD)
Temporal profiling of DNA replication (University of
Promoter activity (Stanford)
DNaseI hypersensitive sites (NHGRI)
Posted on 26 Oct. 2004 - Sequence Freeze For Multiple Alignments
We are pleased to release the first "official" sequence
data freeze for the ENCODE multiple sequence alignment
projects. The data formats are described in the
README file, and the sequences and
supporting information is collected in the
The species included in this freeze are as follows:
You will notice that we have worked hard to include a
number of species for which genome-wide sequence data was
already available. The process by which these orthologous
regions were identified is still an area of active
research development, the details of which will be
presented at the upcoming ENCODE meeting at CSHL.
Please note that we have also included a *second* rat
sequence (ratB) in this freeze. RatB represents an
initiative to standardize the quality level of sequences
in the ENCODE regions for species with genome-wide
sequence data. The data were made available just before
our freeze date, so we decided to include both versions of
the rat sequence for now. Eventually these sequences will
likely be rolled into future genome assemblies.
Remember, this is a work in progress, so not all targets
have sequence from all species. And some species/target
combinations may not be complete yet. Progress on the
NISC-generated sequences can be found at the
NISC ENCODE Project: Comparative
Many people have worked very hard to make these data
available. Special thanks to Daryl Thomas, Kate
Rosenbloom and the entire UCSC Team; Greg Schuler and the
NCBI team; Colin Dewey and Lior Pachter; Pam Thomas and
the NISC team; and David Wheeler and the BCM team.
Please send any comments to the
ENCODE MSA Mailing List.
Elliott H. Margulies, Ph.D.
Genome Technology Branch, NHGRI
Posted on 24 Jun. 2004 - ENCODE Project Portal Released
We are proud to announce the release of features
in the UCSC Genome Browser that are tailored to
the ENCODE project community, including this home
page to consolidate these resources.
The initial resources include sequences for the current
human assemblies (hg16, hg15, hg13, and hg12), sequence of
the comparative species from
tools for coordinate conversion between human
assemblies, format descriptions for data
submission, and contact information for help with
submitting annotation data and analyses.
Bulk downloads of the sequence and annotations may
be obtained from the ENCODE Project
page. The sequences available here are repeat-masked
versions of the GenBank records.