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Sample GSM580032 Query DataSets for GSM580032
Status Public on Aug 16, 2010
Title HCFaa-DS13484
Sample type RNA
Source name Human Cardiac Fibroblasts-Adult Atrial
Organism Homo sapiens
Characteristics cell type: Human Cardiac Fibroblasts-Adult Atrial
Biomaterial provider ScienCell;6320
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_HCFaa_E_100603_29_DS13484_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 72.28593
2315102 41.1687
2315104 109.5279
2315105 47.09207
2315107 275.2241
2315112 61.96769
2315114 24.7668
2315116 41.17976
2315118 916.352
2315120 412.2495
2315126 18.3851
2315132 6.799423
2315138 60.82463
2315140 38.83585
2315142 10.87375
2315144 13.81941
2315146 38.49101
2315148 86.80412
2315149 164.5964
2315150 168.9237

Total number of rows: 1384231

Table truncated, full table size 22720 Kbytes.

Supplementary file Size Download File type/resource
GSM580032_X_Hs_HCFaa_E_100603_29_DS13484_W_3.CEL.gz 23.4 Mb (ftp)(http) CEL
GSM580032_wgEncodeUwAffyExonArrayHcfaaSimpleSignalRep2.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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