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Sample GSM651563 Query DataSets for GSM651563
Status Public on Jan 07, 2011
Title HA-sp-DS14794
Sample type RNA
Source name Human astrocytes, spinal cord
Organism Homo sapiens
Characteristics cell type: Human astrocytes, spinal cord
term: BTO:0000099
Biomaterial provider Sciencell;1820
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, spinal cord
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 101.4844
2315102 101.4889
2315104 97.80138
2315105 44.6434
2315107 279.8904
2315112 79.46323
2315114 37.84358
2315116 19.74877
2315118 902.7885
2315120 363.9368
2315126 13.11122
2315132 10.8033
2315138 74.48873
2315140 82.72778
2315142 11.07036
2315144 9.020471
2315146 54.8397
2315148 158.0344
2315149 175.8277
2315150 198.9321

Total number of rows: 1384231

Table truncated, full table size 22717 Kbytes.

Supplementary file Size Download File type/resource
GSM651563_X_Hs_HAsp_E_100901_10_RS16426_W.CEL.gz 23.6 Mb (ftp)(http) CEL
GSM651563_wgEncodeUwAffyExonArrayHaspSimpleSignalRep2.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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