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Sample GSM824867 Query DataSets for GSM824867
Status Public on Nov 01, 2011
Title HFF-MyC-DS15079
Sample type RNA
 
Source name Human Foreskin Fibroblast Cells Expressing Canine cMyc
Organism Homo sapiens
Characteristics lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: AffyExonArray
datatype description: Affymetrix Exon Microarray
cell: HFF-Myc
cell organism: human
cell description: foreskin fibroblast cells expressing canine cMyc
cell karyotype: normal
cell lineage: fibroblast
cell sex: M
labexpid: RS17570
replicate: 2
Biomaterial provider Dr.Torok-Storb,FHCRC;HFF-Myc
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 75.13527
2315102 66.40823
2315104 80.11858
2315105 35.67311
2315107 108.4743
2315112 80.82538
2315114 62.14052
2315116 49.56557
2315118 1220.55
2315120 452.1721
2315126 15.77828
2315132 10.96377
2315138 90.33013
2315140 48.93182
2315142 4.015826
2315144 7.894348
2315146 40.43341
2315148 84.07904
2315149 203.054
2315150 75.95158

Total number of rows: 1384231

Table truncated, full table size 22778 Kbytes.




Supplementary file Size Download File type/resource
GSM824867_X_Hs_HFF_Myc_E_101230_06_RS17570_W.CEL.gz 23.4 Mb (ftp)(http) CEL
GSM824867_hg19_wgEncodeUwAffyExonArrayHffmycSimpleSignalRep2.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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