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Sample GSM651570 Query DataSets for GSM651570
Status Public on Jan 07, 2011
Title HA-c-DS14770
Sample type RNA
Source name Human astrocytes, cerebellar
Organism Homo sapiens
Characteristics cell type: Human astrocytes, cerebellar
Biomaterial provider Sciencell;1810
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 astrocytes, cerebellar
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 122.927
2315102 42.41677
2315104 121.5091
2315105 42.59496
2315107 233.3062
2315112 116.5829
2315114 55.66045
2315116 59.89731
2315118 858.2695
2315120 471.8465
2315126 16.1202
2315132 10.43763
2315138 101.0349
2315140 60.09261
2315142 18.9916
2315144 7.130478
2315146 31.5092
2315148 143.3044
2315149 159.7997
2315150 122.4557

Total number of rows: 1384231

Table truncated, full table size 22708 Kbytes.

Supplementary file Size Download File type/resource
GSM651570_X_Hs_HAc_E_101115_04_RS17240_W.CEL.gz 23.5 Mb (ftp)(http) CEL
GSM651570_wgEncodeUwAffyExonArrayHacSimpleSignalRep2.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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