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Sample GSM651579 Query DataSets for GSM651579
Status Public on Jan 07, 2011
Title LNCaP-DS14684
Sample type RNA
Source name prostate adenocarcinoma
Organism Homo sapiens
Characteristics cell type: prostate adenocarcinoma
term: BTO:0002021
Biomaterial provider ATCC;CRL-1740
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 prostate adenocarcinoma
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 148.2012
2315102 156.9577
2315104 198.4893
2315105 42.12737
2315107 197.021
2315112 98.28387
2315114 68.47638
2315116 61.06861
2315118 941.2061
2315120 346.5277
2315126 24.00631
2315132 3.27204
2315138 91.85848
2315140 55.00071
2315142 34.27169
2315144 16.1287
2315146 55.49512
2315148 194.8238
2315149 175.7526
2315150 108.0618

Total number of rows: 1384231

Table truncated, full table size 22702 Kbytes.

Supplementary file Size Download File type/resource
GSM651579_X_Hs_LNCAP_E_101115_13_RS17249_W.CEL.gz 23.6 Mb (ftp)(http) CEL
GSM651579_wgEncodeUwAffyExonArrayLncapSimpleSignalRep2.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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