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Sample GSM510534 Query DataSets for GSM510534
Status Public on Feb 17, 2010
Title AG04450-DS12255
Sample type RNA
Source name Fetal lung fibroblast
Organism Homo sapiens
Characteristics cell type: Fetal lung fibroblast
Biomaterial provider Coriell;AG04450
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 Fetal lung fibroblast
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 120.5914
2315102 110.7541
2315104 104.4712
2315105 28.39845
2315107 130.7808
2315114 70.20476
2315126 30.26432
2315132 9.526369
2315133 84.58101
2315134 13.33287
2315138 80.03995
2315140 43.49409
2315142 18.64631
2315144 6.828995
2315146 41.67427
2315148 215.5017
2315149 122.6197
2315150 108.4017
2315151 13.75364
2315153 52.12097

Total number of rows: 1384231

Table truncated, full table size 22742 Kbytes.

Supplementary file Size Download File type/resource
GSM510534_X_Hs_AG04450_E_091208_01_DS12255_W.CEL.gz 23.4 Mb (ftp)(http) CEL
GSM510534_wgEncodeUwAffyExonArrayAg04450SimpleSignalRep2.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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