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Sample GSM472931 Query DataSets for GSM472931
Status Public on Nov 19, 2009
Title GM12878-DS11526
Sample type RNA
Source name lymphoblastoid
Organism Homo sapiens
Characteristics cell type: lymphoblastoid
term: BTO:0002026
Biomaterial provider Coriell;GM12878
Treatment protocol not applicable
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 X_Hs_GM12878_E_090723_04_DS11526_W.CEL
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
Probe group file used for analysis: HuEx-1_0-st-v2.r2.pgf
Submission date Nov 18, 2009
Last update date Apr 23, 2013
Contact name ENCODE DCC
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
VALUE quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

Data table
2315101 40.01246
2315102 45.26317
2315104 40.74583
2315105 19.69964
2315107 122.6024
2315114 50.62243
2315126 21.63374
2315132 3.891582
2315133 42.14842
2315134 0.0001140397
2315138 31.34752
2315140 20.26298
2315142 0.0001362934
2315144 7.317421
2315146 18.83382
2315148 188.5939
2315149 59.30163
2315150 23.80092
2315151 6.044113
2315153 11.99388

Total number of rows: 1384231

Table truncated, full table size 22815 Kbytes.

Supplementary file Size Download File type/resource
GSM472931_X_Hs_GM12878_E_090723_04_DS11526_W.CEL.gz 38.5 Mb (ftp)(http) CEL
GSM472931_wgEncodeUwAffyExonArrayGm12878SimpleSignalRep1.broadPeak.gz 20.9 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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