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Sample GSM824858 Query DataSets for GSM824858
Status Public on Nov 01, 2011
Title PrEC-DS12098
Sample type RNA
 
Source name Human Prostate Epithelial Cell line
Organism Homo sapiens
Characteristics lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: AffyExonArray
datatype description: Affymetrix Exon Microarray
cell: PrEC
cell organism: human
cell description: prostate epithelial cell line
cell karyotype: normal
cell lineage: epithelial
cell sex: U
labexpid: RS19008
replicate: 2
Biomaterial provider Lonza;CC-2555
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 http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwAffyExonArray
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
HuEx-1_0-st-v2.r2.pgf
quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
 
Submission date Oct 31, 2011
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 89.47477
2315102 66.51073
2315104 135.805
2315105 44.07259
2315107 79.71925
2315112 97.71783
2315114 69.69556
2315116 75.69909
2315118 1046.188
2315120 547.1978
2315126 22.51108
2315132 1.798233
2315138 115.2859
2315140 42.79062
2315142 16.44295
2315144 8.54031
2315146 35.23188
2315148 137.9749
2315149 158.2611
2315150 95.95919

Total number of rows: 1384231

Table truncated, full table size 22752 Kbytes.




Supplementary file Size Download File type/resource
GSM824858_X_Hs_PrEC_E_110517_12_RS19008_W.CEL.gz 23.6 Mb (ftp)(http) CEL
GSM824858_hg19_wgEncodeUwAffyExonArrayPrecSimpleSignalRep2.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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