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Sample GSM580005 Query DataSets for GSM580005
Status Public on Aug 16, 2010
Title H7-hESC-DS13133
Sample type RNA
Source name Undifferentiated human embryonic stem cells
Organism Homo sapiens
Characteristics cell type: Undifferentiated human embryonic stem cells
Biomaterial provider WiCell;WA07(H7)
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_hESCT0_E_100603_09_DS13133_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 Aug 16, 2010
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 124.4725
2315102 162.449
2315104 200.1713
2315105 45.67533
2315107 441.1278
2315112 110.4506
2315114 68.04491
2315116 69.46215
2315118 966.9146
2315120 459.353
2315126 31.63479
2315132 13.56716
2315138 109.7402
2315140 56.57552
2315142 9.90157
2315144 22.14644
2315146 72.49117
2315148 178.3619
2315149 275.7409
2315150 133.496

Total number of rows: 1384231

Table truncated, full table size 22702 Kbytes.

Supplementary file Size Download File type/resource
GSM580005_X_Hs_hESCT0_E_100603_09_DS13133_W.CEL.gz 24.1 Mb (ftp)(http) CEL
GSM580005_wgEncodeUwAffyExonArrayH7esSimpleSignalRep2.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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