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Sample GSM580008 Query DataSets for GSM580008
Status Public on Aug 16, 2010
Title HConF-DS11637
Sample type RNA
Source name Human Conjunctival Fibroblast
Organism Homo sapiens
Characteristics cell type: Human Conjunctival Fibroblast
Biomaterial provider ScienCell;6570
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_HConF_E_100603_01_DS11637_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 79.68616
2315102 79.73454
2315104 110.2105
2315105 39.65764
2315107 170.7503
2315112 83.34849
2315114 46.93192
2315116 63.05037
2315118 644.0831
2315120 210.7894
2315126 16.24591
2315132 4.155609
2315138 106.3311
2315140 68.33353
2315142 19.21639
2315144 11.91146
2315146 48.10117
2315148 165.0352
2315149 136.1824
2315150 123.4432

Total number of rows: 1384231

Table truncated, full table size 22709 Kbytes.

Supplementary file Size Download File type/resource
GSM580008_X_Hs_HConF_E_100603_01_DS11637_W.CEL.gz 23.3 Mb (ftp)(http) CEL
GSM580008_wgEncodeUwAffyExonArrayHconfSimpleSignalRep2.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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