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Sample GSM824872 Query DataSets for GSM824872
Status Public on Nov 01, 2011
Title GM12864-DS12431
Sample type RNA
 
Source name B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment: EBV transformed
Organism Homo sapiens
Characteristics lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: AffyExonArray
datatype description: Affymetrix Exon Microarray
cell: GM12864
cell organism: human
cell description: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed
cell lineage: mesoderm
cell sex: M
labexpid: DS12431
replicate: 1
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12864
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 31.40919
2315102 18.25852
2315104 27.04562
2315105 27.16179
2315107 40.87638
2315112 31.0765
2315114 33.24268
2315116 63.75246
2315118 572.0162
2315120 178.4655
2315126 11.95277
2315132 0.0005688217
2315138 21.30293
2315140 14.54226
2315142 0.7392055
2315144 12.0412
2315146 11.0014
2315148 34.43784
2315149 41.59681
2315150 19.00707

Total number of rows: 1384231

Table truncated, full table size 22874 Kbytes.




Supplementary file Size Download File type/resource
GSM824872_X_Hs_GM12864_E_091118_05_DS12431_W.CEL.gz 21.5 Mb (ftp)(http) CEL
GSM824872_hg19_wgEncodeUwAffyExonArrayGm12864SimpleSignalRep1.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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