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Sample GSM651566 Query DataSets for GSM651566
Status Public on Jan 07, 2011
Title RPTEC-DS14065
Sample type RNA
Source name Renal Proximal Tubule Epithelial Cells
Organism Homo sapiens
Characteristics cell type: Renal Proximal Tubule Epithelial Cells
Biomaterial provider Lonza;CC-2553,CC-2553T225
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 Renal Proximal Tubule Epithelial 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 51.60465
2315102 60.46488
2315104 79.23766
2315105 26.56259
2315107 186.2398
2315112 53.25268
2315114 15.153
2315116 24.30346
2315118 821.456
2315120 239.6033
2315126 6.309735
2315132 7.416688
2315138 41.39954
2315140 39.68929
2315142 11.49986
2315144 8.119925
2315146 28.60208
2315148 48.53036
2315149 124.6875
2315150 72.72672

Total number of rows: 1384231

Table truncated, full table size 22742 Kbytes.

Supplementary file Size Download File type/resource
GSM651566_X_Hs_RPTEC_E_100901_13_RS16429_W.CEL.gz 22.6 Mb (ftp)(http) CEL
GSM651566_wgEncodeUwAffyExonArrayRptecSimpleSignalRep2.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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