Duke Affy Exon Track Settings
 
ENCODE Duke Affy All-Exon Arrays   (All Expression tracks)

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 GM12878 Tier1  1  ENCODE Duke Affy All Exon Array Signal Replicate 1 (in GM12878 cells)    Schema   2010-09-16 
 
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 GM12878 Tier1  2  ENCODE Duke Affy All Exon Array Signal Replicate 2 (in GM12878 cells)    Schema   2010-09-16 
 
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 GM12878 Tier1  3  ENCODE Duke Affy All Exon Array Signal Replicate 3 (in GM12878 cells)    Schema   2010-09-16 
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Description

This track displays human tissue microarray data using Affymetrix Human Exon 1.0 ST expression arrays. This RNA expression track was produced as part of the ENCODE Project. RNA was extracted from cells that were also analyzed by DNaseI hypersensitivity, FAIRE, and ChIP (Open Chromatin track).

Display Convention 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 scores between 900-1000 are in the highest 10% quantile for signal value of that particular cell type. Similarly, items scoring 800-900 are the next 10% quantile and at the bottom of scale, items scoring 100-200 are in the lowest 20% 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. Total RNA was isolated from these cells using trizol extraction followed by cleanup on RNEasy column (Qiagen) that included a DNase step. The RNA was checked for quality using a nanodrop and an Agilent Bioanalyzer . RNA (1ug) deemed to be of good quality was then processed according to the standard Affymetrix Whole transcript Sense Target labeling protocol that included a riboreduction step. The fragmented biotin-labeled cDNA was hybridized over 16h to Affymetrix Exon 1.0 ST arrays and scanned on an Affymetrix Scanner 3000 7G using AGCC software. Exon expression analyses were carried out using Affymetrix Expression Console 1.1 software tools. Samples were quantile normalized for background correction and Probe Logarithmic Intensity Error summarized. Only values for the CORE probes were calculated as these seem to be the most robust.

Verification

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

Release Notes

This is Release 2 (June 2011) of this track, which excludes the LHSR cell line (treated and untreated). The data has been withdrawn by the submitting lab for DNase, FAIRE and exon array.

Previous version of these files are available for download from the FTP site.

Credits

RNA was extracted from each cell type by Greg Crawford's group at Duke University. RNA was purified and hybridized to Affymetrix Exon arrays by Sridar Chittur and Scott Tenenbaum at the University of Albany-SUNY. Data analyses were performed by Holly Dressman, Darin London, and Zhancheng Zhang at Duke University.

Contact: Terry Furey

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.