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. The RNA was extracted from cells that were also analyzed by DNaseI hypersensitivity, (Duke DNaseI HS), FAIRE (UNC FAIRE), and ChIP (UTA TFBS).
In contrast to the hg18 annotation, this track now displays exon array data that has been aggregated to the gene level for those probes that have been linked to genes. Probes not linked to genes are displayed at the probe level. The display for this track shows gene 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 in the Expression track group. See Methods for a description as to how probe level data was processed to produce gene level annotations.
Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.
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 DNaseI step. The RNA was checked for quality using a nanodrop and an Agilent Bioanalyzer. RNA (1 µg) 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 16 h 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. All samples were processed together using the sketch-quantile normalization method. Gene level analysis was done at the "extended" annotation confidence level. Probes were summarized with median polish as used in RMA, and the background was corrected with PM and RMA background correction options. And all library files used were default library files. Gene names were assigned based on the output annotation file from this software. The accession number for the annotated transcript was used if a gene name was not assigned. If neither was present, the probe number was used.
Data were verified by analyzing biological replicates displaying Pearson correlation coefficient > 0.9, when replicates were available.
This is release 2 of this track, correcting the cell line Astrocy to NH-A.
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 Zhancheng Zhang (UNC Chapel Hill) and Darin London (Duke University).
Contact: Terry Furey
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.