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Sample GSM580014 Query DataSets for GSM580014
Status Public on Aug 16, 2010
Title HMVEC-dLy-Ad-DS13261
Sample type RNA
 
Source name Normal Adult Human Blood Microvascular Endothelial Cells, Dermal-Derived
Organism Homo sapiens
Characteristics cell type: Normal Adult Human Blood Microvascular Endothelial Cells, Dermal-Derived
Biomaterial provider Lonza;CC-2810,CC-2810T75
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_HMVECdLyAd_E_100603_17_DS13261_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
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 67.73103
2315102 160.4667
2315104 141.5764
2315105 40.77895
2315107 174.0164
2315112 71.71703
2315114 49.38412
2315116 43.71757
2315118 619.0012
2315120 273.7395
2315126 6.124096
2315132 12.68153
2315138 60.82211
2315140 45.20257
2315142 12.69542
2315144 12.9818
2315146 33.90376
2315148 108.0144
2315149 99.37847
2315150 92.43105

Total number of rows: 1384231

Table truncated, full table size 22721 Kbytes.




Supplementary file Size Download File type/resource
GSM580014_X_Hs_HMVECdLyAd_E_100603_17_DS13261_W.CEL.gz 22.8 Mb (ftp)(http) CEL
GSM580014_wgEncodeUwAffyExonArrayHmvecdlyadSimpleSignalRep1.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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