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Sample GSM580022 Query DataSets for GSM580022
Status Public on Aug 16, 2010
Title HMVEC-dBl-Ad-DS13329
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-2811,CC-2811T75
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_HMVECdBlAd_E_100603_18_DS13329_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 65.58829
2315102 72.52763
2315104 73.02932
2315105 22.43889
2315107 144.2567
2315112 47.75692
2315114 27.6235
2315116 25.1789
2315118 387.9468
2315120 309.3511
2315126 6.616668
2315132 0.0001562817
2315138 75.14361
2315140 19.39226
2315142 7.438176
2315144 12.67375
2315146 12.58245
2315148 85.55275
2315149 166.106
2315150 95.97308

Total number of rows: 1384231

Table truncated, full table size 22755 Kbytes.




Supplementary file Size Download File type/resource
GSM580022_X_Hs_HMVECdBlAd_E_100603_18_DS13329_W.CEL.gz 22.5 Mb (ftp)(http) CEL
GSM580022_wgEncodeUwAffyExonArrayHmvecdbladSimpleSignalRep2.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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