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Sample GSM580028 Query DataSets for GSM580028
Status Public on Aug 16, 2010
Title HEK293-DS13691
Sample type RNA
Source name embryonic kidney
Organism Homo sapiens
Characteristics biomaterial_type: immortalized cell line
line: HEK293
cell type: embryonic kidney
term: BTO:0000007
Biomaterial provider ATCC;CRL-1573
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_HEK293_E_100603_37_DS13691_W_3.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 Jul 29, 2016
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 68.99343
2315102 65.82659
2315104 99.07028
2315105 44.66901
2315107 537.6479
2315112 103.1994
2315114 55.34977
2315116 51.65121
2315118 752.8836
2315120 327.6495
2315126 21.51238
2315132 2.495055
2315138 53.01742
2315140 53.35192
2315142 10.10718
2315144 13.60668
2315146 28.11743
2315148 97.88059
2315149 112.3272
2315150 93.48201

Total number of rows: 1384231

Table truncated, full table size 22699 Kbytes.

Supplementary file Size Download File type/resource
GSM580028_X_Hs_HEK293_E_100603_37_DS13691_W_3.CEL.gz 23.3 Mb (ftp)(http) CEL
GSM580028_wgEncodeUwAffyExonArrayHek293SimpleSignalRep2.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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