28 September 2012 - New ENCODE on-line tutorial and Quick Reference Cards
To supplement the existing ENCODE Foundations tutorial, OpenHelix has developed a second
tutorial describing newer ENCODE data and access tools. Slides for this tutorial are freely available from the
website at: http://openhelix.com/ENCODE2.
Also available free (up to 30 cards shipped free in the US) is a Quick Reference Card that
provides a handy summary of access features. For more information see
the OpenHelix announcement.
27 September 2012 - ENCODE data releases: UNC/BSU ProtGenc, UNC FAIRE (Rel 2), HAIB TFBS (Rel 3), CSHL Long RNA-seq (Rel 3)
One new track and three track updates were released on the human hg19 browser:
Proteogenomics Hg19 and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ:
This track displays mass spectrometry data that have been matched to genomic sequences
in GM12878, H1-hESC, H1-neuron, and K562 cell types. Peptides were mapped to an in silico
translation and proteolytic digestion of the whole human genome (UCSC Hg19), and the GENCODE
translation of protein-coding transcripts database. The track can be used to identify which parts
of the genome are translated into proteins, to verify which transcripts discovered by other ENCODE
experiments are protein-coding, to reveal new genes and/or splice variants and proteins with
post-translational modifications (PTM). Of particular interest is the possibility of uncovering the
translation of small open reading frames (ORFs), antisense transcripts, or protein-coding regions
that have been annotated as introns previously.
Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill) (Release 2):
FAIRE (Formaldelhyde-Assisted Isolation of Regulatory Elements) is a method to isolate and identify
nucleosome-depleted regions of the genome. Release 2 of this track contains 12 new experiments,
including 11 new cell lines.
Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB (Release 3):
This release contains 110 new experiments including 3 new cell lines.
There were also data corrections (see Release Notes section for details).
Long RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 3):
This release contains additional files for many experiments including
GENCODE V10 referenced Transcripts, Genes and Exons (previous datasets
referenced GENCODE V7). Complete details are in the track Release Notes.
25 September 2012 - Mouse ENCODE data releases: UW DNaseI DGF, UW DNaseI HS (Rel 2), LICR Histone (Rel 3), CSHL Long RNA-seq (Rel 3)
One new track and three track updates were released on the Mouse mm9 browser.
5 September 2012 - ENCODE results published in Nature, Science and other journals
The results of the ENCODE project were published today in a coordinated set of 30 papers published in multiple journals.