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Sample GSM472941 Query DataSets for GSM472941
Status Public on Nov 19, 2009
Title HGF-DS11752
Sample type RNA
Source name human gingaval fibroblast
Organism Homo sapiens
Characteristics cell type: human gingaval fibroblast
term: BTO:0000519
Biomaterial provider ScienCell;2620
Treatment protocol not applicable
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_HGF_E_091007_05_DS11752_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 Nov 18, 2009
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 56.8338
2315102 48.70781
2315104 62.3273
2315105 48.17458
2315107 114.5961
2315114 74.33659
2315126 8.535504
2315132 7.056432
2315133 63.84653
2315134 2.26608
2315138 46.86356
2315140 12.78473
2315142 10.37344
2315144 13.53015
2315146 16.99631
2315148 123.2627
2315149 114.1893
2315150 56.55608
2315151 0.0001432069
2315153 13.25345

Total number of rows: 1384231

Table truncated, full table size 22821 Kbytes.

Supplementary file Size Download File type/resource
GSM472941_X_Hs_HGF_E_091007_05_DS11752_W.CEL.gz 22.8 Mb (ftp)(http) CEL
GSM472941_wgEncodeUwAffyExonArrayHgfSimpleSignalRep2.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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