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Sample GSM651573 Query DataSets for GSM651573
Status Public on Jan 07, 2011
Title HRGEC-DS13716
Sample type RNA
Source name Human Renal Glomerular Endothelial Cells
Organism Homo sapiens
Characteristics cell type: Human Renal Glomerular Endothelial Cells
Biomaterial provider ScienCell;4000
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 Renal Glomerular Endothelial Cells
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
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 108.5895
2315102 96.30532
2315104 79.42357
2315105 54.33778
2315107 182.0923
2315112 81.35717
2315114 41.3863
2315116 35.8787
2315118 701.4706
2315120 360.1237
2315126 44.10257
2315132 7.801146E-05
2315138 100.7467
2315140 41.87301
2315142 10.24752
2315144 40.28063
2315146 39.87664
2315148 230.4927
2315149 139.7503
2315150 155.6827

Total number of rows: 1384231

Table truncated, full table size 22726 Kbytes.

Supplementary file Size Download File type/resource
GSM651573_X_Hs_HRGEC_E_101115_07_RS17243_W.CEL.gz 23.3 Mb (ftp)(http) CEL
GSM651573_wgEncodeUwAffyExonArrayHrgecSimpleSignalRep2.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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