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Sample GSM510517 Query DataSets for GSM510517
Status Public on Feb 17, 2010
Title HAEpiC-DS12673
Sample type RNA
 
Source name Human Amniotic Epithelial Cells
Organism Homo sapiens
Characteristics cell type: Human Amniotic Epithelial Cells
Biomaterial provider ScienCell;7100
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 Human Amniotic Epithelial Cells
X_Hs_HAEpiC_E_091211_06_DS12673_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 Feb 17, 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 39.07251
2315102 48.52522
2315104 59.28799
2315105 27.26785
2315107 68.99318
2315114 50.20768
2315126 28.66711
2315132 18.31483
2315133 45.53807
2315134 3.516649
2315138 74.31165
2315140 28.23591
2315142 4.987634
2315144 7.787692
2315146 31.91293
2315148 103.4248
2315149 91.07336
2315150 77.71416
2315151 11.44641
2315153 39.66563

Total number of rows: 1384231

Table truncated, full table size 22758 Kbytes.




Supplementary file Size Download File type/resource
GSM510517_X_Hs_HAEpiC_E_091211_06_DS12673_W.CEL.gz 22.8 Mb (ftp)(http) CEL
GSM510517_wgEncodeUwAffyExonArrayHaeSimpleSignalRep2.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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