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Sample GSM281131 Query DataSets for GSM281131
Status Public on Jan 01, 2009
Title GBM DNA hypermethylome: 5-AZA vs mock in U-87 MG
Sample type RNA
 
Channel 1
Source name Mock treated U-87 MG cells
Organism Homo sapiens
Characteristics U-87 MG human GBM cell line
Biomaterial provider Dr. Greg Riggins, Johns Hopkins Oncology Center
Treatment protocol 1x PBS for 96 hours
Growth protocol McCoy's 5A medium with 10% BCS and 1x P/S
Extracted molecule total RNA
Extraction protocol TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment
Label Cy3
Label protocol Agilent low RNA input linear amplification kit
 
Channel 2
Source name 5-AZA treated U-87 MG cells
Organism Homo sapiens
Characteristics U-87 MG human GBM cell line treated with 5-AZA
Biomaterial provider Dr. Greg Riggins, Johns Hopkins Oncology Center
Treatment protocol 5 micromolar 5-AZA for 96 hours
Growth protocol McCoy's 5A medium with 10% BCS and 1x P/S
Extracted molecule total RNA
Extraction protocol TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment
Label Cy5
Label protocol Agilent low RNA input linear amplification kit
 
 
Hybridization protocol Agilent Gene Expression Hybridization Kit using manufacturer's protocol (G4140-90050)
Scan protocol Microarrays are scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays. with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays.
Description Identification of the GBM DNA hypermethylome revealed by gene expression profiling: 5-AZA vs mock in U-87 MG
Data processing Log ratio of red signal to green signal was calculated after loess normalization as implemented in the Limma package from Bioconductor
 
Submission date Apr 11, 2008
Last update date Dec 22, 2008
Contact name Leander Van Neste
Organization name Ghent University
Department Molecular Biotechnology
Lab Bioinformatics and Computational Genomics
Street address Coupure Links 653
City Ghent
ZIP/Postal code 9000
Country Belgium
 
Platform ID GPL4133
Series (1)
GSE11233 The Cancer Genome Atlas (TCGA) Consortium Integrated DNA Methylation Analysis

Data table header descriptions
ID_REF
VALUE log2 ratio of normalized Cy5 intensity to normalized Cy3 intensity
CH1_SIG_MEDIAN Median spot value of channel 1
CH1_BKD_MEDIAN Background median spot value of channel 1
CH2_SIG_MEDIAN Median spot value of channel 2
CH2_BKD_MEDIAN Background median spot value of channel 2

Data table
ID_REF VALUE CH1_SIG_MEDIAN CH1_BKD_MEDIAN CH2_SIG_MEDIAN CH2_BKD_MEDIAN
1 -0.211018400711706 74301.2 43 124026 58
2 -0.0374861180721355 73 45 69 57
3 0.0433999222701223 71 46 71 57
4 0.0393559449423217 73 44 75 58
5 0.0755199784911479 73 45 78 59
6 0.0552024611315988 71.5 45 73 60
7 -0.0411133151595858 77 45 77 60
8 0.0393559449423217 73 45 75 59
9 -0.085489674163619 79 46 77.5 58
10 -0.0520917177410681 76 45 74 59
11 -0.0292155415633701 77 46 78 60
12 0.0278802131452616 2035 46 4394 61
13 -0.26529983044148 134 46 181 60
14 0.0209443775440683 649 45 1399.5 60
15 0.0986187300952203 118 45 205 59
16 0.612113107957369 14052.5 46 42711.1 61
17 -0.122358075554674 130 46 196 59
18 -0.655433810107107 250 45 305 59
19 -0.229508988533104 34604.5 46 57941.4 61
20 -0.144873860939311 141 46 217.5 61

Total number of rows: 45220

Table truncated, full table size 1798 Kbytes.




Supplementary file Size Download File type/resource
GSM281131.txt.gz 13.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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