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.