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ENCODE UW Affy All-Exon Arrays   (All Expression tracks)

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 GM12878  1  ENCODE UW Affy All-Exon Array Signal Replicate 1 (in GM12878 cells)    Schema   2010-06-21 
 
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 K562  1  ENCODE UW Affy All-Exon Array Signal Replicate 1 (in K562 cells)    Schema   2010-04-02 
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Description

This track displays human tissue microarray data using Affymetrix Human Exon 1.0 GeneChip. The track was produced as part of the ENCODE Project.

Release Notes

This is release 2 of this track. 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).

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, turn on the Affy Exon Probes track, which can be found inside the Affy Exon supertrack in the "Expression" track group.

Methods

Cells were grown according to the approved ENCODE cell culture protocols. A subset of the cells was stored frozen in RNALater. Total RNA was labeled and hybridized to Affymetrix Human Exon 1.0 ST arrays. 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.

Verification

Data were verified by sequencing biological replicates displaying correlation coefficient >0.9.

Credits

These data were generated by the University of Washington ENCODE group.

Contact: Richard Sandstrom

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.