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Sample GSM510519 Query DataSets for GSM510519
Status Public on Feb 17, 2010
Title HIPEpiC-DS12699
Sample type RNA
 
Source name Human Iris Pigment Epithelial Cells
Organism Homo sapiens
Characteristics cell type: Human Iris Pigment Epithelial Cells
Biomaterial provider ScienCell;6560
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 Iris Pigment Epithelial Cells
X_Hs_HIPEpiC_E_091214_07_DS12699_W.CEL
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
E-mail(s) encode-help@lists.stanford.edu
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
ID_REF
VALUE quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

Data table
ID_REF VALUE
2315101 64.79617
2315102 88.72862
2315104 58.09687
2315105 43.11194
2315107 24.5667
2315114 8.303859
2315126 14.2426
2315132 6.89033E-05
2315133 81.47929
2315134 1.854877
2315138 54.59645
2315140 30.14657
2315142 12.78235
2315144 6.666876
2315146 28.61849
2315148 114.7729
2315149 66.93349
2315150 38.59465
2315151 16.76394
2315153 19.30178

Total number of rows: 1384231

Table truncated, full table size 22798 Kbytes.




Supplementary file Size Download File type/resource
GSM510519_X_Hs_HIPEpiC_E_091214_07_DS12699_W.CEL.gz 22.7 Mb (ftp)(http) CEL
GSM510519_wgEncodeUwAffyExonArrayHipeSimpleSignalRep2.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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