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Series GSE19090 Query DataSets for GSE19090
Status Public on Nov 19, 2009
Title Exon arrays of ENCODE tier 1, tier 2 and tier 3 cell types
Project ENCODE
Organism Homo sapiens
Experiment type Expression profiling by array
Summary This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom If you have questions about the Genome Browser track associated with this data, contact ENCODE (

At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 106 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 manufacturers protocol. Intensity files from the scanned exon arrays were sent to our lab for analysis at the exon level (Affymetrix ExACT 1.2.1 software). Samples were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized.

For data usage terms and conditions, please refer to and
Overall design Continuing exon profiling of ENCODE approved cell types, these coincide with DNaseI hypersensitivity sequencing assays, ChIP-seq (histone modifications, transcription factors), and other ENCODE assay types.
Web link
Contributor(s) Stamatoyannopoulos JA
Citation(s) 19966280, 22955617
BioProject PRJNA30709
Submission date Nov 18, 2009
Last update date Jul 29, 2016
Contact name ENCODE DCC
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
Platforms (1)
GPL5188 [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version]
Samples (182)
GSM472898 BJ-DS7708
GSM472900 Caco-2-DS8235
GSM472901 GM12878-DS8623

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE19090_RAW.tar 8.3 Gb (http)(custom) TAR (of BED, BROADPEAK, CEL)
Processed data included within Sample table
Processed data provided as supplementary file

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