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Sample GSM580016 Query DataSets for GSM580016
Status Public on Aug 16, 2010
Title HMVEC-dNeo-DS12929
Sample type RNA
 
Source name Normal Neonatal Human Microvascular Endothelial Cells (single Donnor), Dermal-Derived
Organism Homo sapiens
Characteristics cell type: Normal Neonatal Human Microvascular Endothelial Cells (single Donnor), Dermal-Derived
Biomaterial provider Lonza;CC-2505,CC-2505T225
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_HMVECdNeo_E_100603_07_DS12929_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 85.002
2315102 224.7198
2315104 292.1278
2315105 43.44014
2315107 286.3864
2315112 61.34754
2315114 52.53353
2315116 58.49102
2315118 950.6658
2315120 377.7122
2315126 8.621742
2315132 4.893369
2315138 52.81726
2315140 38.19973
2315142 17.26343
2315144 13.58827
2315146 42.52061
2315148 75.8261
2315149 145.7888
2315150 119.1869

Total number of rows: 1384231

Table truncated, full table size 22740 Kbytes.




Supplementary file Size Download File type/resource
GSM580016_X_Hs_HMVECdNeo_E_100603_07_DS12929_W.CEL.gz 23.3 Mb (ftp)(http) CEL
GSM580016_wgEncodeUwAffyExonArrayHmvecdneoSimpleSignalRep2.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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