ENCODE University of Washington Affymetrix Exon Array: Detailed methods

At cell harvest, a subset of cells was stored at -20 degrees C in RNALater.
Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according
to vendor recommended protocols.  Total RNA quality was assessed on RNA 6000
Nano Chips (Agilent) using a Bioanalyzer (Agilent).  Approximately 3ug of
total RNA for each cell type was sent to the Center for Array Technology (CAT)
for labeling and hybridization to Affymetrix Human Exon 1.0 ST arrays.  Briefly,
a Whole Transcript Sense Target Labeling Assay (Affymetrix) was used by the CAT
to reduce the rRNA, perform in vitro transcription (IVT) and create labeled
sense strand DNA for hybridization to the arrays.  Hybridizations were carried
out according the manufacturer's protocol.  

Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix
ExACT 1.2.1 software) and the gene level (Affymetrix Expression Console 1.1
software).  Samples were quantile normalized with PM-GCBG background correction
and PLIER (Probe Logarithmic Intensity Error) summarized.