Description
This track displays human tissue microarray data using
Affymetrix Human Exon 1.0 GeneChip
and was produced as part of the ENCODE Project.
This track in the hg19 assembly is a continuation of the work displayed in
the hg18 assembly with additional cell lines.
Display Conventions and Configuration
The display for this track shows probe location and signal value
as grayscale-colored items where higher
signal values correspond to darker-colored blocks. Items with score of 1000
are in the highest 10% quantile for signal value of that particular cell type.
Similarly, items scoring 900 are the next 10% quantile and at the bottom of
scale, items scoring 100 are in the lowest 10% quantile for signal value.
The subtracks within this composite annotation track correspond to data from
different cell types and tissues. The configuration options are
shown at the top of the track description page, followed by a list of
subtracks.
To display only selected subtracks, uncheck the boxes next to the tracks you
wish to hide.
For information regarding specific microarray probes, look under the
"Expression" track group and turn on the
Affy Exon Array track.
Metadata for a particular subtrack can be found by clicking the down arrow
in the list of subtracks.
Methods
Cells were grown according to the approved
ENCODE cell culture protocols.
A subset of the cells were stored frozen in RNAlater. For the WI-38 Tamoxifen-treated
(4OHTAM_20nM_72hr)
cell type, cells at 50-80% confluency were treated for 72 hours with 20 nM
4-hydroxytamoxifen in growth medium (from a 1000X working stock in absolute ethanol).
At harvest, greater than 95% of DNA synthesis was inhibited and the cells had
an induced fusiform/round morphology with greater than 95% showing dramatic
senescence-associated heterochromatic foci. Total RNA was labeled and hybridized
to Affymetrix Human Exon 1.0 ST V2 arrays using hg19 probesets. Exon and gene level
expression analysis were carried out using Affymetrix ExACT 1.2.1 and Affymetrix
Expression Console 1.1 software tools. Samples were quantile normalized for
background correction and Probe Logarithmic Intensity Error summarized.
More detailed methods are
here.
Release Notes
This is release 4 (Jul 2012) of this track. A patch update has removed previously released
K562 zinc-finger experiments due to a data merging issue. This update adds in H7-hESC cells that have been differentiated with different time courses.
Verification
Data were verified by sequencing biological replicates displaying correlation
coefficient of 0.9 or greater.
Credits
These data were generated by the University of Washington ENCODE group.
Contact: Richard Sandstrom
References
Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA.
Sequencing newly replicated DNA reveals widespread plasticity in human replication timing.
Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):139-44.
Data Release Policy
Data users may freely use ENCODE data, but may not, without prior
consent, submit publications that use an unpublished ENCODE dataset until
nine months following the release of the dataset. This date is listed in
the Restricted Until column, above. The full data release policy
for ENCODE is available
here.