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Sample GSM510515 Query DataSets for GSM510515
Status Public on Feb 17, 2010
Title HRPEpiC-DS12568
Sample type RNA
Source name Human Retinal Pigment Epithelial Cells
Organism Homo sapiens
Characteristics cell type: Human Retinal Pigment Epithelial Cells
Biomaterial provider ScienCell;6540
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 Retinal Pigment 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 146.426
2315102 161.2572
2315104 167.2474
2315105 66.14336
2315107 131.3596
2315114 50.58179
2315126 31.94013
2315132 9.182071
2315133 159.1215
2315134 10.00323
2315138 123.9461
2315140 32.94938
2315142 52.19173
2315144 19.38282
2315146 61.92817
2315148 299.0003
2315149 227.3356
2315150 164.6441
2315151 20.27056
2315153 56.84214

Total number of rows: 1384231

Table truncated, full table size 22711 Kbytes.

Supplementary file Size Download File type/resource
GSM510515_X_Hs_HRPEpiC_E_091211_03_DS12568_W.CEL.gz 24.3 Mb (ftp)(http) CEL
GSM510515_wgEncodeUwAffyExonArrayHrpeSimpleSignalRep2.broadPeak.gz 21.1 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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