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Sample GSM472921 Query DataSets for GSM472921
Status Public on Nov 19, 2009
Title HRCE-DS10666
Sample type RNA
Source name human renal cortical epithelial cells
Organism Homo sapiens
Characteristics cell type: human renal cortical epithelial cells
term: BTO:0000059
Biomaterial provider Lonza;CC-2554
Treatment protocol not applicable
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 X_Hs_HRCE_E_090616_06_DS10666_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 Nov 18, 2009
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 60.86971
2315102 42.60992
2315104 53.90954
2315105 28.54259
2315107 118.6598
2315114 38.87572
2315126 13.63588
2315132 18.11467
2315133 65.51136
2315134 1.450631
2315138 64.61121
2315140 45.60712
2315142 9.334433
2315144 22.52329
2315146 35.90575
2315148 74.65428
2315149 77.62521
2315150 78.55817
2315151 6.621872
2315153 6.116378

Total number of rows: 1384231

Table truncated, full table size 22801 Kbytes.

Supplementary file Size Download File type/resource
GSM472921_X_Hs_HRCE_E_090616_06_DS10666_W.CEL.gz 39.2 Mb (ftp)(http) CEL
GSM472921_wgEncodeUwAffyExonArrayHrceSimpleSignalRep2.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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