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Sample GSM651581 Query DataSets for GSM651581
Status Public on Jan 07, 2011
Title WI-38-DS14320
Sample type RNA
Source name Embryonic Lung Fibroblast Cells, hTERT, GFP-RAF-ER
Organism Homo sapiens
Characteristics cell type: Embryonic Lung Fibroblast Cells, hTERT, GFP-RAF-ER
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
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 124.2546
2315102 77.1105
2315104 93.14942
2315105 41.35161
2315107 283.3
2315112 109.1634
2315114 79.03803
2315116 36.24077
2315118 922.4248
2315120 472.8417
2315126 21.61753
2315132 19.87094
2315138 92.47141
2315140 48.17778
2315142 19.83892
2315144 15.21367
2315146 23.99611
2315148 205.564
2315149 166.5138
2315150 147.192

Total number of rows: 1384231

Table truncated, full table size 22706 Kbytes.

Supplementary file Size Download File type/resource
GSM651581_X_Hs_WI38_E_101115_15_RS17251_W.CEL.gz 23.9 Mb (ftp)(http) CEL
GSM651581_wgEncodeUwAffyExonArrayWi38SimpleSignalRep2.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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