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Sample GSM510574 Query DataSets for GSM510574
Status Public on Feb 17, 2010
Title HEEpiC-DS12763
Sample type RNA
Source name Human Esophageal Epithelial Cells
Organism Homo sapiens
Characteristics cell type: Human Esophageal Epithelial Cells
Biomaterial provider ScienCell;2700
Growth protocol Followed vendor recommendations for growth protocol/media
Extracted molecule total RNA
Extraction protocol At cell harvest, a subset of cells was stored at -20oC 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).
Label biotin
Label protocol A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.
Hybridization protocol Hybridizations were carried out according the manufacturer (Affymetrix) protocol
Scan protocol Affymterix Gene Chip Scanner 3000
Description Human Esophageal Epithelial Cells
Data processing Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
Probe group file used for analysis: HuEx-1_0-st-v2.r2.pgf
Submission date Feb 17, 2010
Last update date Apr 23, 2013
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
Platform ID GPL5188
Series (1)
GSE19090 Exon arrays of ENCODE tier 1, tier 2 and tier 3 cell types

Data table header descriptions
VALUE quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

Data table
2315101 81.34269
2315102 43.82238
2315104 80.88531
2315105 34.58524
2315107 88.45287
2315114 54.3128
2315126 25.24425
2315132 6.892205
2315133 91.37714
2315134 5.78053
2315138 49.54928
2315140 32.58115
2315142 3.195045
2315144 33.81132
2315146 49.67912
2315148 147.3915
2315149 76.32104
2315150 146.3972
2315151 14.21939
2315153 58.78136

Total number of rows: 1384231

Table truncated, full table size 22723 Kbytes.

Supplementary file Size Download File type/resource
GSM510574_X_Hs_HEEpiC_E_091214_08_DS12763_W.CEL.gz 23.3 Mb (ftp)(http) CEL
GSM510574_wgEncodeUwAffyExonArrayHeeSimpleSignalRep2.broadPeak.gz 21.0 Mb (ftp)(http) BROADPEAK
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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