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Sample GSM580036 Query DataSets for GSM580036
Status Public on Aug 16, 2010
Title HPF-DS13380
Sample type RNA
Source name Human Pulmonary Fibroblasts
Organism Homo sapiens
Characteristics cell type: Human Pulmonary Fibroblasts
Biomaterial provider ScienCell;3300
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_HPF_E_100603_24_DS13380_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
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 66.72346
2315102 108.9919
2315104 110.7233
2315105 30.65874
2315107 117.3228
2315112 80.49648
2315114 27.01045
2315116 27.59226
2315118 531.2428
2315120 185.7281
2315126 27.64778
2315132 8.708405
2315138 95.60614
2315140 32.17291
2315142 19.00418
2315144 2.450517
2315146 68.83739
2315148 165.3818
2315149 128.8268
2315150 131.4142

Total number of rows: 1384231

Table truncated, full table size 22764 Kbytes.

Supplementary file Size Download File type/resource
GSM580036_X_Hs_HPF_E_100603_24_DS13380_W.CEL.gz 22.5 Mb (ftp)(http) CEL
GSM580036_wgEncodeUwAffyExonArrayHpfSimpleSignalRep2.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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