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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 19, 2009 |
| Title |
Exon arrays of ENCODE tier 1, tier 2 and tier 3 cell types |
| Project |
ENCODE
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| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom mailto:sull@u.washington.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).
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 http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| 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.
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| Web link |
http://www.ncbi.nlm.nih.gov/projects/geo/info/ENCODE.html
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| Contributor(s) |
Stamatoyannopoulos JA |
| Citation(s) |
19966280, 22955617 |
| BioProject |
PRJNA30709 |
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| Submission date |
Nov 18, 2009 |
| Last update date |
Jul 29, 2016 |
| Contact name |
ENCODE DCC |
| E-mail(s) |
encode-help@lists.stanford.edu
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| Organization name |
ENCODE DCC
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| Street address |
300 Pasteur Dr
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5120 |
| Country |
USA |
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| Platforms (1) |
| GPL5188 |
[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version] |
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| Samples (182)
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| 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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