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Sample GSM472925 Query DataSets for GSM472925
Status Public on Nov 19, 2009
Title BJ-DS11523
Sample type RNA
Source name skin fibroblast
Organism Homo sapiens
Characteristics cell type: skin fibroblast
term: BTO:0001255
Biomaterial provider ATCC;CRL-2522
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_BJ_E_090716_04_DS11523_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 30.97391
2315102 56.99134
2315104 54.31781
2315105 37.09533
2315107 64.06712
2315114 40.74755
2315126 29.15177
2315132 4.058441
2315133 45.62619
2315134 6.706876E-05
2315138 41.26225
2315140 41.7986
2315142 0.0001507932
2315144 6.235821
2315146 11.11302
2315148 59.93901
2315149 76.60332
2315150 40.4097
2315151 3.331999
2315153 21.07861

Total number of rows: 1384231

Table truncated, full table size 22853 Kbytes.

Supplementary file Size Download File type/resource
GSM472925_X_Hs_BJ_E_090716_04_DS11523_W.CEL.gz 37.9 Mb (ftp)(http) CEL
GSM472925_wgEncodeUwAffyExonArrayBjSimpleSignalRep2.broadPeak.gz 20.9 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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