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Sample GSM580024 Query DataSets for GSM580024
Status Public on Aug 16, 2010
Title HMVEC-dBl-Neo-DS13233
Sample type RNA
 
Source name Normal Neonatal Human Blood Microvascular Endothelial Cells, Dermal-Derived
Organism Homo sapiens
Characteristics cell type: Normal Neonatal Human Blood Microvascular Endothelial Cells, Dermal-Derived
Biomaterial provider Lonza;CC-2813,CC-2813T75
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_HMVECdBlNeo_E_100603_14_DS13233_W_2.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 94.10735
2315102 180.0389
2315104 217.6507
2315105 46.74579
2315107 362.4089
2315112 77.77035
2315114 27.57585
2315116 24.58078
2315118 815.0222
2315120 515.3718
2315126 22.67061
2315132 3.104943
2315138 189.1693
2315140 55.23936
2315142 15.40943
2315144 7.479466
2315146 54.87452
2315148 116.3599
2315149 203.9024
2315150 201.3574

Total number of rows: 1384231

Table truncated, full table size 22751 Kbytes.




Supplementary file Size Download File type/resource
GSM580024_X_Hs_HMVECdBlNeo_E_100603_14_DS13233_W_2.CEL.gz 23.7 Mb (ftp)(http) CEL
GSM580024_wgEncodeUwAffyExonArrayHmvecdblneoSimpleSignalRep2.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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