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Sample GSM472904 Query DataSets for GSM472904
Status Public on Nov 19, 2009
Title GM06990-DS7784
Sample type RNA
Source name lymphoblastoid
Organism Homo sapiens
Characteristics cell type: lymphoblastoid
term: BTO:0002062
Biomaterial provider Coriell;GM06990
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_GM69_E_080117_02_DS7784_D.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 70.43857
2315102 96.00692
2315104 136.7531
2315105 29.87463
2315107 124.0701
2315114 63.52377
2315126 9.26027
2315132 1.342705
2315133 32.34298
2315134 3.301797
2315138 42.34025
2315140 9.636159
2315142 2.817827
2315144 5.340936
2315146 21.20563
2315148 73.01622
2315149 77.68105
2315150 46.82702
2315151 22.81488
2315153 19.88889

Total number of rows: 1384231

Table truncated, full table size 22840 Kbytes.

Supplementary file Size Download File type/resource
GSM472904_X_Hs_GM69_E_080117_02_DS7784_D.CEL.gz 39.0 Mb (ftp)(http) CEL
GSM472904_wgEncodeUwAffyExonArrayGm06990SimpleSignalRep2.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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