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Sample GSM472907 Query DataSets for GSM472907
Status Public on Nov 19, 2009
Title HepG2-DS7768
Sample type RNA
Source name liver carcinoma
Organism Homo sapiens
Characteristics cell type: liver carcinoma
term: BTO:0000559
Biomaterial provider ATCC;HB-8065
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_HEPG_E_080602_01_DS7768_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 68.28957
2315102 67.5323
2315104 64.62691
2315105 45.20263
2315107 94.68564
2315114 40.13989
2315126 13.23109
2315132 3.261331
2315133 98.03548
2315134 6.647608
2315138 81.84585
2315140 41.93402
2315142 6.982654
2315144 4.614762
2315146 18.04184
2315148 102.3808
2315149 90.2086
2315150 36.76006
2315151 16.00294
2315153 11.88788

Total number of rows: 1384231

Table truncated, full table size 22819 Kbytes.

Supplementary file Size Download File type/resource
GSM472907_X_Hs_HEPG_E_080602_01_DS7768_W.CEL.gz 39.4 Mb (ftp)(http) CEL
GSM472907_wgEncodeUwAffyExonArrayHepg2SimpleSignalRep2.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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