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Sample GSM824865 Query DataSets for GSM824865
Status Public on Nov 01, 2011
Title HFF-DS15119
Sample type RNA
 
Source name Human Foreskin Fibroblast
Organism Homo sapiens
Characteristics lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: AffyExonArray
datatype description: Affymetrix Exon Microarray
cell: HFF
cell organism: human
cell description: foreskin fibroblast
cell karyotype: normal
cell sex: M
labexpid: RS17568
replicate: 2
Biomaterial provider Dr.Torok-Storb,FHCRC;HFF
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 70.87392
2315102 49.37454
2315104 56.24624
2315105 41.20795
2315107 122.859
2315112 62.59705
2315114 70.77264
2315116 57.28214
2315118 641.6713
2315120 283.4872
2315126 11.6775
2315132 0.0002577863
2315138 71.82629
2315140 38.22649
2315142 7.282521
2315144 16.35332
2315146 29.37044
2315148 80.79098
2315149 77.62518
2315150 101.21

Total number of rows: 1384231

Table truncated, full table size 22791 Kbytes.




Supplementary file Size Download File type/resource
GSM824865_X_Hs_HFF_E_101230_04_RS17568_W.CEL.gz 22.8 Mb (ftp)(http) CEL
GSM824865_hg19_wgEncodeUwAffyExonArrayHffSimpleSignalRep2.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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