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Sample GSM580010 Query DataSets for GSM580010
Status Public on Aug 16, 2010
Title HMVEC-LLy-DS13193
Sample type RNA
Source name Normal Human Lymphatic Microvascular Endothelial Cells, Lung-Derived
Organism Homo sapiens
Characteristics cell type: Normal Human Lymphatic Microvascular Endothelial Cells, Lung-Derived
Biomaterial provider Lonza;CC-2814, CC-2814T25
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_HMVECLly_E_100603_13_DS13193_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 100.2624
2315102 212.4391
2315104 193.4023
2315105 33.00104
2315107 304.0223
2315112 81.50806
2315114 58.42144
2315116 60.9528
2315118 969.8209
2315120 451.2499
2315126 8.644895
2315132 4.85833
2315138 112.4878
2315140 34.75813
2315142 11.77015
2315144 10.78041
2315146 70.29326
2315148 135.0194
2315149 160.9218
2315150 131.6648

Total number of rows: 1384231

Table truncated, full table size 22706 Kbytes.

Supplementary file Size Download File type/resource
GSM580010_X_Hs_HMVECLly_E_100603_13_DS13193_W_2.CEL.gz 23.5 Mb (ftp)(http) CEL
GSM580010_wgEncodeUwAffyExonArrayHmvecllySimpleSignalRep2.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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