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Sample GSM824870 Query DataSets for GSM824870
Status Public on Nov 01, 2011
Title WERI-Rb-1-DS13674
Sample type RNA
 
Source name retinoblastoma (PMID: 844036)
Organism Homo sapiens
Characteristics lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: AffyExonArray
datatype description: Affymetrix Exon Microarray
cell: WERI-Rb-1
cell organism: human
cell description: retinoblastoma (PMID: 844036)
cell karyotype: cancer
cell lineage: ectoderm
cell sex: F
labexpid: RS17575
replicate: 1
Biomaterial provider ATCC;HTB-169
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 137.1991
2315102 189.9593
2315104 245.403
2315105 48.82061
2315107 226.9669
2315112 79.18615
2315114 98.1264
2315116 178.7242
2315118 1133.579
2315120 496.1736
2315126 20.65646
2315132 6.925478
2315138 75.84464
2315140 59.99796
2315142 13.85108
2315144 11.78134
2315146 68.14408
2315148 132.0544
2315149 194.3272
2315150 76.82719

Total number of rows: 1384231

Table truncated, full table size 22695 Kbytes.




Supplementary file Size Download File type/resource
GSM824870_X_Hs_WERI_E_101230_11_RS17575_W.CEL.gz 24.2 Mb (ftp)(http) CEL
GSM824870_hg19_wgEncodeUwAffyExonArrayWerirb1SimpleSignalRep1.broadPeak.gz 21.1 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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