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Sample GSM651577 Query DataSets for GSM651577
Status Public on Jan 07, 2011
Title HUVEC-DS13475
Sample type RNA
 
Source name Human Umbilical Vein Endothelial Cell
Organism Homo sapiens
Characteristics cell type: Human Umbilical Vein Endothelial Cell
term: BTO:0001949
Biomaterial provider Lonza;CC-2517
Treatment protocol For WI-38 cell type, Tamoxifen treated replicates only: induce senescence, cells at 50-80% confluency are treated for 72 hours with 20nM 4-hydroxytamoxifen in growth medium (from a 1000X working stock in absolute ethanol). At harvest, greater than 95% of DNA synthesis is inhibited and the cells have an induced fusiform/round morphology with greater than 95% showing dramatic senescence-associated heterochromatic foci
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 Human Umbilical Vein Endothelial Cell
X_Hs_HUVEC_E_101115_11_RS17247_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 Jan 07, 2011
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 76.67079
2315102 71.24233
2315104 92.33877
2315105 29.70062
2315107 242.5012
2315112 92.54086
2315114 54.241
2315116 46.7359
2315118 884.3427
2315120 413.9737
2315126 18.36896
2315132 15.07686
2315138 64.73788
2315140 62.27348
2315142 19.06192
2315144 16.24399
2315146 40.92779
2315148 98.55174
2315149 143.1089
2315150 128.9524

Total number of rows: 1384231

Table truncated, full table size 22692 Kbytes.




Supplementary file Size Download File type/resource
GSM651577_X_Hs_HUVEC_E_101115_11_RS17247_W.CEL.gz 23.7 Mb (ftp)(http) CEL
GSM651577_wgEncodeUwAffyExonArrayHuvecSimpleSignalRep2.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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