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Sample GSM580012 Query DataSets for GSM580012
Status Public on Aug 16, 2010
Title HMVEC-dLy-Neo-DS13146
Sample type RNA
 
Source name Normal Neonatal Human Lymphatic Microvascular Endothelial Cells, Dermal-Derived
Organism Homo sapiens
Characteristics cell type: Normal Neonatal Human Lymphatic Microvascular Endothelial Cells, Dermal-Derived
Biomaterial provider Lonza;CC-2812,CC-2812T25
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_HMVECdLyNeo_E_100603_10_DS13146_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 88.13313
2315102 228.6964
2315104 221.8964
2315105 52.3749
2315107 119.4455
2315112 59.73781
2315114 38.46966
2315116 46.22052
2315118 786.643
2315120 357.24
2315126 13.53348
2315132 5.494188
2315138 80.79762
2315140 37.34155
2315142 10.22965
2315144 13.89333
2315146 48.33463
2315148 115.0213
2315149 157.0276
2315150 165.3816

Total number of rows: 1384231

Table truncated, full table size 22715 Kbytes.




Supplementary file Size Download File type/resource
GSM580012_X_Hs_HMVECdLyNeo_E_100603_10_DS13146_W.CEL.gz 23.2 Mb (ftp)(http) CEL
GSM580012_wgEncodeUwAffyExonArrayHmvecdlyneoSimpleSignalRep2.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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