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Sample GSM281132 Query DataSets for GSM281132
Status Public on Jan 01, 2009
Title GBM DNA hypermethylome: TSA 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 TSA treated U-87 MG cells
Organism Homo sapiens
Characteristics U-87 MG human GBM cell line treated with TSA
Biomaterial provider Dr. Greg Riggins, Johns Hopkins Oncology Center
Treatment protocol 300 nanomolar TSA for 18 hour
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: TSA 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 -0.0687513953244556 69804.5 45 194857 58
2 -0.110161483969916 81 46 75 59
3 -0.0863957525128941 80 46 75 58
4 -0.0117019824145401 79 46 79 59
5 -0.0356985326867529 80 46 79 61
6 -0.0875388848844572 83 47 80.5 59
7 -0.107874979245730 82 47 77 59
8 -0.017013711065088 81 46 82.5 60
9 -0.143779342666328 83 46 76 59
10 -0.12065541599373 82 47 76 59
11 0.036588795304873 79 47 83 59
12 -1.33460694603491 1970 47 1565 58
13 -0.432108320959182 144 47 155 59
14 -0.24806567359904 611 48 977 59
15 -0.106190162442349 114 47 143 58
16 0.46423759860102 13051 46 44349 60
17 -0.133915031644110 140.5 46 193.5 58
18 -0.425245148932374 250 48 323 59
19 0.643252701336781 26641 46 111985 60
20 -0.0388104109926458 145.5 47 220.5 59

Total number of rows: 45220

Table truncated, full table size 1798 Kbytes.




Supplementary file Size Download File type/resource
GSM281132.txt.gz 13.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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