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Sample GSM580034 Query DataSets for GSM580034
Status Public on Aug 16, 2010
Title HPAF-DS13416
Sample type RNA
 
Source name Human Pulmonary Artery Fibroblasts
Organism Homo sapiens
Characteristics cell type: Human Pulmonary Artery Fibroblasts
Biomaterial provider ScienCell;3120
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_HPAF_E_100603_27_DS13416_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 Aug 16, 2010
Last update date Apr 23, 2013
Contact name ENCODE DCC
E-mail(s) encode-help@lists.stanford.edu
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
ID_REF
VALUE quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

Data table
ID_REF VALUE
2315101 89.50813
2315102 108.2414
2315104 112.8019
2315105 35.48767
2315107 314.0967
2315112 98.43432
2315114 44.03986
2315116 46.77225
2315118 836.0034
2315120 260.7789
2315126 10.61922
2315132 4.069263
2315138 88.2302
2315140 53.44697
2315142 14.71103
2315144 8.127715
2315146 60.50816
2315148 85.09113
2315149 112.5772
2315150 187.4068

Total number of rows: 1384231

Table truncated, full table size 22713 Kbytes.




Supplementary file Size Download File type/resource
GSM580034_X_Hs_HPAF_E_100603_27_DS13416_W.CEL.gz 23.2 Mb (ftp)(http) CEL
GSM580034_wgEncodeUwAffyExonArrayHpafSimpleSignalRep2.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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