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Sample GSM580030 Query DataSets for GSM580030
Status Public on Aug 16, 2010
Title AoAF-DS13513
Sample type RNA
Source name Normal Human Aortic Adventitial Fibroblast Cells
Organism Homo sapiens
Characteristics cell type: Normal Human Aortic Adventitial Fibroblast Cells
Biomaterial provider Lonza;CC-7014,CC-7014T75
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_AoAF_E_100603_30_DS13513_W_3.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 Aug 16, 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 59.74062
2315102 22.79756
2315104 90.64974
2315105 30.22057
2315107 230.8214
2315112 59.06501
2315114 29.79052
2315116 33.2443
2315118 593.789
2315120 197.199
2315126 12.22265
2315132 2.297906
2315138 56.2827
2315140 37.75576
2315142 17.22128
2315144 15.13881
2315146 32.27535
2315148 75.38045
2315149 106.4133
2315150 106.4555

Total number of rows: 1384231

Table truncated, full table size 22759 Kbytes.

Supplementary file Size Download File type/resource
GSM580030_X_Hs_AoAF_E_100603_30_DS13513_W_3.CEL.gz 22.7 Mb (ftp)(http) CEL
GSM580030_wgEncodeUwAffyExonArrayAoafSimpleSignalRep2.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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