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Sample GSM651583 Query DataSets for GSM651583
Status Public on Jan 07, 2011
Title WI-38-DS14328
Sample type RNA
 
Source name Embryonic Lung Fibroblast Cells, hTERT, GFP-RAF-ER, treated with Tamoxifen
Organism Homo sapiens
Characteristics cell type: Embryonic Lung Fibroblast Cells, hTERT, GFP-RAF-ER, treated with Tamoxifen
Biomaterial provider SBIGeM, Dr.Carl Mann
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 Embryonic Lung Fibroblast Cells, hTERT, GFP-RAF-ER, treated with Tamoxifen
X_Hs_WI38_E_101115_17_RS17253_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 120.4721
2315102 117.3241
2315104 126.0701
2315105 40.23914
2315107 298.5558
2315112 96.4539
2315114 71.21575
2315116 27.19821
2315118 1315.685
2315120 552.8944
2315126 24.0379
2315132 6.027795
2315138 66.66364
2315140 61.36929
2315142 33.78417
2315144 12.19458
2315146 65.56779
2315148 114.5689
2315149 142.0622
2315150 143.6963

Total number of rows: 1384231

Table truncated, full table size 22720 Kbytes.




Supplementary file Size Download File type/resource
GSM651583_X_Hs_WI38_E_101115_17_RS17253_W.CEL.gz 23.8 Mb (ftp)(http) CEL
GSM651583_wgEncodeUwAffyExonArrayWi38OhtamSimpleSignalRep2.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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