12 Sept 2013 - New UDR ENCODE Download Method Available
The UCSC Genome Browser is pleased to offer a new download protocol to use when downloading
large sets of files from our download servers: UDR (UDT Enabled Rsync). UDR utilizes rsync
as the transport mechanism, but sends the data over the UDT protocol, which enables huge
amounts of data to be downloaded more efficiently over long distances.
25 July 2013 - BLUEPRINT Epigenome Data Hub and Quick Reference PDF Now Available
We are pleased to announce the addition of the
BLUEPRINT Epigenomics Data Hub on the UCSC Genome Browser through our
function. All data were produced and processed by the European
BLUEPRINT Epigenome project,
aimed to generate 100 reference epigenomes from distinct types of haematopoietic cells and
their malignant leukaemic counterparts. Please send any data related questions to
firstname.lastname@example.org. The BLUEPRINT Hub currently contains 8 DNase-seq, 48 DNA methylation,
170 Histone modification, and 24 RNA-seq tracks, focused on displaying variation in human
monocyte and neutrophil cells from 7 adult blood and 4 cord blood samples. Future releases
of data for additional samples are planned at a regular basis.
Also the ENCODE Quick Reference Card is now available in
PDF courtesy of OpenHelix on the
ENCODE Education and Outreach page.
28 May 2013 - ENCODE portal changes: New Link to NHGRI Tutorials, New External
Software Tools Page, Updates to Publications including New 2013 Consortium Papers Section
The ENCODE portal was updated to include informative new and expanded pages.
A new link to the NHGRI ENCODE Tutorials was added to the
ENCODE Education and Outreach page.
A new External Software Tools
page was added to expand the existing ENCODE Software Tools
resources page. The Publications page was expanded to include a new
2013 Consortium-funded section
and updated with several new references as well as the non-ENCODE Publications page.
Lastly other pages were updated with new information including the ENCODE Analysis Software page, and Quality Metrics page.
13 May 2013 - Uniform Peaks of Transcription Factor ChIP-seq from ENCODE/Analysis
UCSC has released a new browser track containing 690 datasets of transcription factor ChIP-seq
peaks based on data from all five ENCODE TFBS ChIP-seq production groups from the project
inception in 2007 through the ENCODE March 2012 data freeze.
The track covers 161 unique regulatory factors (generic and sequence-specific factors),
spanning 91 human cell types, some under various treatment conditions.
Transcription Factor ChIP-seq Uniform Uniform Peaks from ENCODE/Analysis
File selection tool
This track represents peak calls (regions of enrichment) generated by the ENCODE Analysis Working
Group (AWG) using the uniform processing pipeline developed for the ENCODE Integrative Analysis
effort and published in a set of coordinated papers in September 2012. Peak calls from that
effort (based on datasets from the January 2011 ENCODE data freeze) are available at the
ENCODE Analysis Data Hub.
The new Uniform TFBS track at UCSC includes newer data, slightly modified processing methods,
and improved metadata. Quality metrics are included in metadata, with detailed metrics in a
quality spreadsheet linked to the track description.
Browser users will see the uniform peaks first when using track search for TFBS, and
this track is now the default track shown when the ENCODE TF Binding menu item is
selected in the browser.
The primary and lab-processed data (along with methods descriptions, credits and references)
on which this track is based are available in the following ENCODE tracks: HAIB TFBS, SYDH TFBS,
UChicago TFBS, UTA TFBS, UW CTCF Binding. Many thanks to Anshul Kundaje of the ENCODE AWG
for providing the uniform peaks data, description, and quality spreadsheets.
7 April 2013 - User Resources and Frequently Asked Questions page added to website
This new page provides links to
ENCODE informational material and tools at the NHGRI,
GEO, UCSC, and Nature, together with links to some of the most useful pages at encodeproject.org.
It also includes a helpful FAQ section culled from ENCODE questions received on the ENCODE and
Genome Browser mailing lists.