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Sample GSM580020 Query DataSets for GSM580020
Status Public on Aug 16, 2010
Title HMVEC-LBl-DS13375
Sample type RNA
Source name Normal Human Blood Microvascular Endothelial Cells, Lung-Derived
Organism Homo sapiens
Characteristics cell type: Normal Human Blood Microvascular Endothelial Cells, Lung-Derived
Biomaterial provider Lonza;CC-2815,CC-2815T75
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_HMVECLBl_E_100603_23_DS13375_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
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 108.979
2315102 146.2086
2315104 168.273
2315105 51.68754
2315107 156.5653
2315112 105.8394
2315114 41.20285
2315116 58.88233
2315118 761.9284
2315120 399.2309
2315126 48.82252
2315132 12.78496
2315138 188.6274
2315140 46.98565
2315142 17.38019
2315144 12.54225
2315146 86.70779
2315148 170.808
2315149 253.6001
2315150 196.1056

Total number of rows: 1384231

Table truncated, full table size 22679 Kbytes.

Supplementary file Size Download File type/resource
GSM580020_X_Hs_HMVECLBl_E_100603_23_DS13375_W_2.CEL.gz 23.6 Mb (ftp)(http) CEL
GSM580020_wgEncodeUwAffyExonArrayHmveclblSimpleSignalRep2.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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