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Sample GSM510564 Query DataSets for GSM510564
Status Public on Feb 17, 2010
Title HNPCEpiC-DS12471
Sample type RNA
Source name Human Non-Pigment Ciliary Epithelial Cells
Organism Homo sapiens
Characteristics cell type: Human Non-Pigment Ciliary Epithelial Cells
Biomaterial provider ScienCell;6580
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 Non-Pigment Ciliary 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 90.21942
2315102 89.32227
2315104 99.37037
2315105 56.13808
2315107 173.6315
2315114 72.49045
2315126 32.41866
2315132 13.79359
2315133 134.1571
2315134 1.035518
2315138 119.6761
2315140 43.35232
2315142 15.57353
2315144 20.74791
2315146 64.99294
2315148 248.2723
2315149 229.4165
2315150 102.8518
2315151 7.877839
2315153 45.9039

Total number of rows: 1384231

Table truncated, full table size 22723 Kbytes.

Supplementary file Size Download File type/resource
GSM510564_X_Hs_HNPCEpiC_E_091211_02_DS12471_W.CEL.gz 24.2 Mb (ftp)(http) CEL
GSM510564_wgEncodeUwAffyExonArrayHnpceSimpleSignalRep2.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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