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Sample GSM510521 Query DataSets for GSM510521
Status Public on Feb 17, 2010
Title AG10803-DS12374
Sample type RNA
Source name Adult human abdominal skin fibroblasts
Organism Homo sapiens
Characteristics cell type: Adult human abdominal skin fibroblasts
Biomaterial provider Coriell;AG10803
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 Adult human abdominal skin fibroblasts
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 39.03235
2315102 26.97432
2315104 45.53233
2315105 32.50254
2315107 38.79875
2315114 10.69048
2315126 14.09959
2315132 9.290413E-05
2315133 28.27472
2315134 4.99691E-05
2315138 20.32773
2315140 10.63023
2315142 6.808178
2315144 14.44622
2315146 8.464105
2315148 61.11614
2315149 61.39029
2315150 49.11909
2315151 12.46963
2315153 16.76278

Total number of rows: 1384231

Table truncated, full table size 22903 Kbytes.

Supplementary file Size Download File type/resource
GSM510521_X_Hs_AG10803_E_091118_03_DS12374_W.CEL.gz 21.4 Mb (ftp)(http) CEL
GSM510521_wgEncodeUwAffyExonArrayAg10803SimpleSignalRep2.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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